• using R Under development (unstable) (2012-02-09 r58307)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘Deducer/DESCRIPTION’ ... OK
• this is package ‘Deducer’ version ‘0.5-1’
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... NOTE
  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.
• checking for executable files ... OK
• checking whether package ‘Deducer’ can be installed ... [9s/38s] WARNING
  Found the following significant warnings:
  Warning: Problem initiating JRI. Make sure you built R with shared libraries The Java GUI will not be available.
  See ‘/data/gannet/tmp/ripley/R/packages/tests-devel/Deducer.Rcheck/00install.out’ for details.
• checking installed package size ... NOTE
  installed size is 6.2Mb
  sub-directories of 1Mb or more:
  java 4.4Mb
  javasrc 1.6Mb
• 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 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 ‘Deducer/R/zzz.R’:
  .onLoad calls:
  cat("\nNamespace for JGR could not be found\n")
  cat("\nLoading Deducer without GUI. If you wish the GUI to load, run options(DeducerNoGUI=FALSE) before loading Deducer\n")
  cat("\nNOTE: Environmental variable NOAWT set. Loading Deducer without GUI.\n")
  cat("\nWarning: Problem initiating JRI. The Java GUI will not be available.\n")
  print(jriOK)
  cat("\nWarning: Problem initiating JRI. Make sure you built R with shared libraries The Java GUI will not be available.\n")
  print(jriOK)
  cat("Warning: Unable to start Deducer's Java class. The Java GUI will not be available.")
  print(deducer)
  cat("\n\nDeducer has been loaded from within the Windows Rgui. \n\t\t\t\tFor the best experience, you are encouraged to use JGR console which can be\n\t\t\t\tdownloaded from: http://jgr.markushelbig.org/\n")
  cat("\n\nNote Non-JGR console detected:\n\tDeducer is best used from within JGR (http://jgr.markushelbig.org/).\n\t\t\t\t\t\t\tTo Bring up GUI dialogs, type deducer().\n")
  
  Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
  See section ‘Good practice’ in ?.onAttach.
  
  Found the following possibly unsafe calls:
  File 'R/zzz.R':
  found unlockBinding(".jgr.works", jgrEnv)
  add.chi.squared : <anonymous>: warning in chi.squared.test(x,
  conservative = conservative, sim = TRUE, B = B): partial argument
  match of 'sim' to 'simulate.p.value'
  get.objects: warning in ls(env = env): partial argument match of 'env'
  to 'envir'
  ggcorplot: no visible binding for global variable ‘x_var’
  ggcorplot: no visible binding for global variable ‘y_var’
  ggcorplot: no visible binding for global variable ‘trans’
  ggcorplot: no visible binding for global variable ‘rsq’
  ggcorplot: no visible binding for global variable ‘p’
  ggcorplot: no visible binding for global variable ‘x_label’
  onesample.plot: no visible binding for global variable ‘Value’
  onesample.plot: no visible binding for global variable ‘..density..’
  onesample.plot: warning in position_jitter(h = 0): partial argument
  match of 'h' to 'height'
  oneway.plot: no visible binding for global variable ‘Factor’
  oneway.plot: no visible binding for global variable ‘Value’
  oneway.plot: warning in position_jitter(h = 0): partial argument match
  of 'h' to 'height'
  plot.cor.matrix: no visible binding for global variable ‘x.o’
  plot.cor.matrix: no visible binding for global variable ‘y.o’
  rocplot: no visible binding for global variable ‘Spec’
  rocplot: no visible binding for global variable ‘Sens’
  Found .Internal call in the following function:
  ‘perm.t.test’
  
  Packages should not call .Internal(): it is not part of the API, for
  use only by R itself and subject to change without notice.
• 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 ... WARNING
  ‘library’ or ‘require’ call not declared from: ‘hexbin’
• checking examples ... [33s/100s] OK
• checking PDF version of manual ... OK
  WARNING: There were 2 warnings.
  NOTE: There were 3 notes.
  See
  ‘/data/gannet/tmp/ripley/R/packages/tests-devel/Deducer.Rcheck/00check.log’
  for details.