• using R Under development (unstable) (2012-05-22 r59405)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘pequod/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘pequod’ version ‘0.0-2’
• 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 ‘pequod’ 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 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 ... NOTE
  print.summary.lmres: warning in pf(x$fstatistic[1], x$fstatistic[2],
  x$fstatistic[3], lower = F): partial argument match of 'lower' to
  'lower.tail'
  print.summary.lmres: warning in printCoefmat(Fs, P.value = TRUE,
  has.Pvalue = TRUE, justify = "centre", digits = 3): partial argument
  match of 'P.value' to 'P.values'
  print.summary.lmres: warning in printCoefmat(x$coefficients, P.value =
  TRUE, has.Pvalue = TRUE, na.print = ""): partial argument match of
  'P.value' to 'P.values'
  print.summary.lmres: warning in printCoefmat(x$stat, P.value = TRUE,
  has.Pvalue = TRUE, justify = "centre"): partial argument match of
  'P.value' to 'P.values'
  print.summary.lmres: warning in printCoefmat(Fs, P.value = TRUE,
  has.Pvalue = TRUE, justify = "centre", digits = 3, na.print = ""):
  partial argument match of 'P.value' to 'P.values'
  print.summary.simpleSlope: warning in printCoefmat(x$simple_slope,
  P.value = TRUE, has.Pvalue = TRUE, justify = "centre", digits = 3):
  partial argument match of 'P.value' to 'P.values'
  print.summary.simpleSlope: warning in printCoefmat(x$delta_slope,
  P.value = TRUE, has.Pvalue = TRUE, justify = "centre"): partial
  argument match of 'P.value' to 'P.values'
  summary.lmres: warning in pf(fstatistic[1], fstatistic[2],
  fstatistic[3], lower = F): partial argument match of 'lower' to
  'lower.tail'
  PlotSlope: no visible binding for global variable ‘yini’
  PlotSlope: no visible binding for global variable ‘yend’
• 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 'summary.lmres':
  ‘summary.lmres’
  
  S3 methods shown with full name in documentation object 'summary.simpleSlope':
  ‘summary.simpleSlope’
  
  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 examples ... OK
• checking PDF version of manual ... OK
  NOTE: There were 2 notes.
  See
  ‘/data/gannet/tmp/ripley/R/packages/tests-devel/pequod.Rcheck/00check.log’
  for details.