• using R Under development (unstable) (2012-02-07 r58290)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘lodplot/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘lodplot’ version ‘1.1’
• 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 ‘lodplot’ 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 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
  chromosome.viewlinkage: no visible binding for global variable
  ‘chrom.bands’
  chromosome.viewsequence: no visible binding for global variable
  ‘chrom.bands’
  paint.chromosome: no visible binding for global variable ‘chrom.bands’
  plot.scan: warning in grid.layout(nr = 1, nc = 3, widths =
  unit(chrom.rel.size$r1, "null")): partial argument match of 'nr' to
  'nrow'
  plot.scan: warning in grid.layout(nr = 1, nc = 3, widths =
  unit(chrom.rel.size$r1, "null")): partial argument match of 'nc' to
  'ncol'
  plot.scan: warning in grid.layout(nr = 1, nc = 4, widths =
  unit(chrom.rel.size$r2, "null")): partial argument match of 'nr' to
  'nrow'
  plot.scan: warning in grid.layout(nr = 1, nc = 4, widths =
  unit(chrom.rel.size$r2, "null")): partial argument match of 'nc' to
  'ncol'
  plot.scan: warning in grid.layout(nr = 1, nc = 7, widths =
  unit(chrom.rel.size$r3, "null")): partial argument match of 'nr' to
  'nrow'
  plot.scan: warning in grid.layout(nr = 1, nc = 7, widths =
  unit(chrom.rel.size$r3, "null")): partial argument match of 'nc' to
  'ncol'
  plot.scan: warning in grid.layout(nr = 1, nc =
  length(chrom.rel.size$r4), widths = unit(chrom.rel.size$r4, "null")):
  partial argument match of 'nr' to 'nrow'
  plot.scan: warning in grid.layout(nr = 1, nc =
  length(chrom.rel.size$r4), widths = unit(chrom.rel.size$r4, "null")):
  partial argument match of 'nc' to 'ncol'
  plot.scan: warning in matplot(pos, lod, t = "l", ylim = c(min.stat,
  hi.lod), axes = FALSE, col = col, lwd = lwd, xlab = paste("Genome
  scan position (", units, ")", sep = ""), ylab = "lod score", ...):
  partial argument match of 't' to 'type'
• 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 'plot.scan':
  ‘plot.scan’
  
  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 ... WARNING
  Warning: large data file(s) saved inefficiently:
  size ASCII compress
  chrom.bands.rda 393Kb FALSE none
  
  Note: significantly better compression could be obtained
  by using R CMD build --resave-data
  old_size new_size compress
  chrom.bands.rda 393Kb 47Kb xz
• checking examples ... OK
• checking PDF version of manual ... OK
  WARNING: There was 1 warning.
  NOTE: There were 3 notes.
  See
  ‘/data/gannet/tmp/ripley/R/packages/tests-devel/lodplot.Rcheck/00check.log’
  for details.