• using R Under development (unstable) (2012-02-06 r58287)
• using platform: i686-pc-linux-gnu (32-bit)
• using session charset: UTF-8
• checking for file ‘BARD/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘BARD’ version ‘1.24’
• 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 ‘BARD’ can be installed ... OK
• checking installed package size ... NOTE
  installed size is 7.6Mb
  sub-directories of 1Mb or more:
  doc 3.1Mb
  shapefiles 3.6Mb
• 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 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
  File ‘BARD/R/zzz.R’:
  .onAttach calls:
  print(utils::citation("BARD"))
  
  Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
  See section ‘Good practice’ in ?.onAttach.
  
  PMPreport: warning in scorePlans(tmpPlan, scoreFUN = scoreFUN): partial
  argument match of 'scoreFUN' to 'scoreFUNs'
  PMPreport: warning in scorePlans(tmpPlan, scoreFUN = sFUN): partial
  argument match of 'scoreFUN' to 'scoreFUNs'
  bardClusterExport : gets: warning in assign(n, v, env = .GlobalEnv):
  partial argument match of 'env' to 'envir'
  bardClusterExport: warning in get(name, env = .GlobalEnv): partial
  argument match of 'env' to 'envir'
  lapplyBardCluster.snow: no visible binding for global variable
  ‘clusterApplyLB’
  lapplyBardCluster.snow: no visible binding for global variable
  ‘parLapply’
  plot.grob: no visible global function definition for ‘grid.draw’
  refineGenoudPlan: warning in genoud(fn = genoudScoreFun, nvars =
  length(plan), pop.size = pop.size, hard.generation.limit = FALSE,
  max.generations = max.generations, wait.generation =
  wait.generations, MemoryMatrix = memMat, cluster = genCluster, P3 =
  0, P7 = 0, P4 = 0, P8 = 0, Domains = t(replicate(length(plan), c(1,
  ndists))), solution.tolerance = 0.001, boundary.enforcement = 2,
  print.level = print.level, data.type.int = T, starting.values =
  c(as.double(plan))): partial argument match of 'wait.generation' to
  'wait.generations'
  reportPlans: no visible global function definition for ‘HTMLInitFile’
  reportPlans: no visible global function definition for ‘HTML.title’
  reportPlans: no visible global function definition for ‘HTMLEndFile’
  sdf2bard: no visible global function definition for ‘spTransform’
  startBardCluster: no visible global function definition for
  ‘makeSOCKcluster’
  startBardCluster: no visible global function definition for ‘parLapply’
  stopBardCluster: no visible global function definition for
  ‘stopCluster’
• 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 ... NOTE
  S3 methods shown with full name in documentation object 'nb2graph':
  ‘neighbors.nb’
  
  S3 methods shown with full name in documentation object 'basem<-.default':
  ‘basem<-.default’ ‘basem.default’
  
  The \usage entries for S3 methods should use the \method markup and not
  their full name.
  See the chapter ‘Writing R documentation files’ in the ‘Writing R
  Extensions’ manual.
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking for portable compilation flags in Makevars ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking compiled code ... OK
• checking sizes of PDF files under ‘inst/doc’ ... NOTE
  ‘qpdf’ made some significant size reductions:
  compacted ‘bardJSS.pdf’ from 1.3Mb to 1.2Mb
  consider running tools::compactPDF() on these files
• checking installed files from ‘inst/doc’ ... NOTE
  The following files are already in R: ‘jss.bst’
  Please remove them from your package.
  The following files should probably not be installed:
  ‘Makefile.alt’, ‘article.tex’, ‘bookreview.tex’, ‘codesnippet.tex’,
  ‘fig_example.pdf’
  The following directories should probably not be installed:
  ‘JSSstyle’
  
  Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
  or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
• checking examples ... ERROR
  Running examples in ‘BARD-Ex.R’ failed
  The error occurred in:
  
  
  R Under development (unstable) (2012-02-06 r58287)
  Copyright (C) 2012 The R Foundation for Statistical Computing
  ISBN 3-900051-07-0
  Platform: i686-pc-linux-gnu (32-bit)
  
  R is free software and comes with ABSOLUTELY NO WARRANTY.
  You are welcome to redistribute it under certain conditions.
  Type 'license()' or 'licence()' for distribution details.
  
  Natural language support but running in an English locale
  
  R is a collaborative project with many contributors.
  Type 'contributors()' for more information and
  'citation()' on how to cite R or R packages in publications.
  
  Type 'demo()' for some demos, 'help()' for on-line help, or
  'help.start()' for an HTML browser interface to help.
  Type 'q()' to quit R.
  
  > pkgname <- "BARD"
  > source(file.path(R.home("share"), "R", "examples-header.R"))
  > options(warn = 1)
  > library('BARD')
  Loading required package: digest
  Error in loadNamespace(name) : there is no package called ‘R2HTML’
  Error: package/namespace load failed for ‘BARD’
  Execution halted