• using R Under development (unstable) (2012-05-19 r59366)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘surveillance/DESCRIPTION’ ... OK
• this is package ‘surveillance’ version ‘1.2-1’
• package encoding: latin1
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... WARNING
  As from R 2.14.0 all packages need a namespace.
  One will be generated on installation, but it is better to handcraft a
  NAMESPACE file: R CMD build will produce a suitable starting point.
  CRAN requires a NAMESPACE file for all submissions.
• checking for executable files ... OK
• checking whether package ‘surveillance’ can be installed ... 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 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 ... NOTE
  File ‘surveillance/R/zzz.R’:
  .First.lib calls:
  library(spc)
  library(maptools)
  library(msm)
  
  Package startup functions should not change the search path.
  See section ‘Good practice’ in ?.onAttach.
  
  aggregate.disProg: warning in apply(x$observed, MAR = 1, sum): partial
  argument match of 'MAR' to 'MARGIN'
  aggregate.disProg: warning in apply(x$state, MAR = 1, sum): partial
  argument match of 'MAR' to 'MARGIN'
  hcl.colors: warning in heat_hcl(ncolors, h = c(0, 120), c = c(90, 30),
  l = c(50, 90), power = c(0.75, 1.2)): partial argument match of 'c'
  to 'c.'
  hcl.colors: warning in heat_hcl(ncolors, h = c(0, 120), c = 0, l =
  c(50, 90), power = c(0.75, 1.2)): partial argument match of 'c' to
  'c.'
  init.sts: warning in ts(matrix(rep(state, nAreas), ncol = nAreas, byrow
  = FALSE), freq = frequency(observed)): partial argument match of
  'freq' to 'frequency'
  sumNeighbours: warning in apply(observed[, disProgObj$neighbourhood[,
  i] == 1], MAR = 1, sum): partial argument match of 'MAR' to 'MARGIN'
• 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 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 use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking compiled code ... WARNING
  File ‘/home/hornik/tmp/R.check/r-devel/Work/build/Packages/surveillance/libs/surveillance.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Object: ‘twins.o’
  
  Compiled code should not call functions which might terminate R nor
  write to stdout/stderr instead of to the console.
  
  See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
• checking sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... NOTE
  The following files should probably not be installed:
  ‘apalike.bst’, ‘chicago.bst’, ‘comment.sty’, ‘natbib.sty’,
  ‘pdftricks.sty’
  The following directories should probably not be installed:
  ‘figs’
  
  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 ‘surveillance-Ex.R’ failed
  The error most likely occurred in:
  
  > ### Name: stcd
  > ### Title: Spatio-temporal cluster detection
  > ### Aliases: stcd
  > ### Keywords: cluster
  >
  > ### ** Examples
  >
  > library("splancs")
  
  Spatial Point Pattern Analysis Code in S-Plus
  
  Version 2 - Spatial and Space-Time analysis
  
  > data(burkitt)
  >
  > # order the times
  > burkitt <- burkitt[order(burkitt$t), ]
  >
  > #Parameters for the SR detection
  > epsilon <- 0.5 # relative change within the cluster
  > radius <- 20 # radius
  > threshold <- 161 # threshold limit
  >
  > res <- stcd(x=burkitt$x,
  + y=burkitt$y,
  + t=burkitt$t,
  + radius=radius,
  + epsilon=epsilon,
  + areaA=1,
  + areaAcapBk=1,
  + threshold=threshold)