• using R version 2.14.1 Patched (2012-02-04 r58267)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘gplots/DESCRIPTION’ ... OK
• this is package ‘gplots’ version ‘2.10.1’
• 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 ‘gplots’ 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 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
  barplot2.default: warning in matrix(w.m, nc = NC): partial argument
  match of 'nc' to 'ncol'
  ooplot.default: warning in matrix(w.m, nc = NC): partial argument match
  of 'nc' to 'ncol'
  plotCI: multiple local function definitions for ‘myarrows’ with
  different formal arguments
  sinkplot: warning in exists(".sinkplot.conn", env = globalenv()):
  partial argument match of 'env' to 'envir'
  sinkplot: warning in get(".sinkplot.conn", env = globalenv()): partial
  argument match of 'env' to 'envir'
  sinkplot: warning in get(".sinkplot.data", env = globalenv()): partial
  argument match of 'env' to 'envir'
  sinkplot: warning in exists(".sinkplot.data", env = globalenv()):
  partial argument match of 'env' to 'envir'
• 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 'boxplot.n':
  ‘boxplot.n’
  
  S3 methods shown with full name in documentation object 'plot.lm2':
  ‘plot.lm2’
  
  S3 methods shown with full name in documentation object 'qqnorm.aov':
  ‘qqnorm.aov’
  
  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 ... NOTE
  ‘library’ or ‘require’ call not declared from: ‘MASS’
  ‘data(package=)’ call not declared from: ‘MASS’
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking sizes of PDF files under ‘inst/doc’ ... OK
• checking examples ... OK
• checking for unstated dependencies in tests ... OK
• checking tests ... OK
  Running ‘heatmap2Test.R’
  Comparing ‘heatmap2Test.Rout’ to ‘heatmap2Test.Rout.save’ ...10,13d9
  < The following object(s) are masked from 'package:stats':
  <
  < nobs
  <
  132c128
  < .. | | |--leaf "Lincoln Continental" ( value.Lincoln Continental = 66.1 )
  ---
  > .. | | |--leaf "Lincoln Continental" ( value.Lincoln Continental = 66 )
  146c142
  < .. | | |--leaf "Valiant" ( value.Valiant = 35 )
  ---
  > .. | | |--leaf "Valiant" ( value.Valiant = 35.0 )
  149c145
  < .. | |--[dendrogram w/ 2 branches and 2 members at h = 14, midpoint = 0.5, value = 93.2]
  ---
  > .. | |--[dendrogram w/ 2 branches and 2 members at h = 14.0, midpoint = 0.5, value = 93.2]
  154c150
  < .. | `--[dendrogram w/ 2 branches and 2 members at h = 0.983, midpoint = 0.5, value = 92.9]
  ---
  > .. | `--[dendrogram w/ 2 branches and 2 members at h = 0.983, midpoint = 0.5, value = 93]
  158c154
  < .. |--[dendrogram w/ 2 branches and 4 members at h = 14.8, midpoint = 0.875, value = 74.9]
  ---
  > .. |--[dendrogram w/ 2 branches and 4 members at h = 14.8, midpoint = 0.875, value = 75]
  165c161
  < .. `--[dendrogram w/ 2 branches and 12 members at h = 113, midpoint = 2.3, value = 334]
  ---
  > .. `--[dendrogram w/ 2 branches and 12 members at h = 113, midpoint = 2.30, value = 334]
  Running ‘heatmap_to_heatmap.2_test.R’
  Running ‘plotmeans_nobars.R’
• checking PDF version of manual ... OK