* using log directory 'd:/Rcompile/CRANpkg/local/2.15/lodplot.Rcheck'
* using R version 2.15.0 (2012-03-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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.
CRAN requires a NAMESPACE file for all submissions.
* checking whether package 'lodplot' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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     46Kb       xz
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  'd:/Rcompile/CRANpkg/local/2.15/lodplot.Rcheck/00check.log'
for details.