• using R version 2.14.1 (2011-12-22)
• using platform: i386-apple-darwin9.8.0 (32-bit)
• using session charset: ASCII
• checking for file 'LDheatmap/DESCRIPTION' ... OK
• this is package 'LDheatmap' version '0.9'
• checking package namespace information ... OK
• checking package dependencies ... NOTE
  Packages suggested but not available for checking:
  'rtracklayer' 'GenomicRanges' 'chopsticks'
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking whether package 'LDheatmap' 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
  LDheatmap: no visible global function definition for 'ld.snp'
  plotGenes: no visible global function definition for 'browserSession'
  plotGenes: no visible global function definition for 'genome<-'
  plotGenes: no visible global function definition for 'ucscTableQuery'
  plotGenes: no visible global function definition for
  'GRangesForUCSCGenome'
  plotGenes: no visible global function definition for 'IRanges'
  plotGenes: no visible global function definition for 'getTable'
  plotGenes: no visible global function definition for 'tableNames'
  recombRate: no visible global function definition for 'browserSession'
  recombRate: no visible global function definition for 'genome<-'
  recombRate: no visible global function definition for 'ucscTableQuery'
  recombRate: no visible global function definition for
  'GRangesForUCSCGenome'
  recombRate: no visible global function definition for 'IRanges'
  recombRate: no visible global function definition for 'getTable'
• 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 ... OK
• 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 ... ERROR
  Running examples in 'LDheatmap-Ex.R' failed
  The error most likely occurred in:
  
  > ### Name: GIMAP5.CEU
  > ### Title: Example data set for LDheatmap
  > ### Aliases: GIMAP5.CEU
  > ### Keywords: datasets
  >
  > ### ** Examples
  >
  > data(GIMAP5.CEU)
  > LDheatmap(GIMAP5.CEU$snp.data,GIMAP5.CEU$snp.support$Position)
  Loading required package: chopsticks
  Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
  there is no package called 'chopsticks'
  Error in LDheatmap(GIMAP5.CEU$snp.data, GIMAP5.CEU$snp.support$Position) :
  could not find function "ld.snp"
  Execution halted
• elapsed time (check, wall clock): 0:15