• using R Under development (unstable) (2012-02-27 r58511)
• using platform: x86_64-pc-mingw32 (64-bit)
• using session charset: ISO8859-1
• checking for file 'bams/DESCRIPTION' ... OK
• this is package 'bams' version '1.0'
• 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 whether package 'bams' can be installed ... OK
• checking installed package size ... NOTE
  installed size is 8.3Mb
  sub-directories of 1Mb or more:
  data 7.6Mb
• 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
  ** checking whether the namespace can be loaded with stated dependencies ... OK
  ** checking whether the namespace 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 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
  exportData: no visible binding for global variable 'neuroblastoma'
  geom_tallrect: no visible global function definition for 'proto'
  geom_tallrect: no visible binding for global variable 'GeomRect'
  geom_tallrect : draw_groups: no visible global function definition for
  'unit'
  run.cghseg : <anonymous> : <anonymous>: no visible binding for global
  variable 'begin'
  run.smoothers: no visible binding for global variable 'annotation'
  runglad: no visible binding for global variable 'position'
  runglad: no visible binding for global variable 'logratio'
  runglad: no visible binding for global variable 'chromosome'
• 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 installed files from 'inst/doc' ... OK
• checking examples ...
  ** running examples for arch 'i386' ... ERROR
  Running examples in 'bams-Ex.R' failed
  The error most likely occurred in:
  
  > ### Name: neuroblastoma
  > ### Title: Neuroblastoma copy number profiles and breakpoint annotations
  > ### Aliases: neuroblastoma
  > ### Keywords: datasets
  >
  > ### ** Examples
  >
  > data(neuroblastoma)
  > pids <- levels(neuroblastoma$profiles$profile.id)[1:2]
  > pro <- subset(neuroblastoma$profiles,profile.id%in%pids)
  > ann <- subset(neuroblastoma$annotations,profile.id%in%pids)
  > library(ggplot2)
  > ggplot()+
  + geom_tallrect(aes(xmin=min/1e6,xmax=max/1e6,
  + fill=annotation),data=ann)+
  + geom_point(aes(position/1e6,logratio),pch=1,data=pro)+
  + scale_fill_manual(values=c(breakpoint="red",
  + normal="yellow"))+
  + scale_x_continuous(breaks=c(100,200))+
  + facet_grid(profile.id~chromosome,
  + scales="free_x",space="free")+
  + theme_bw()+
  + opts(axis.title.x=theme_text(vjust = 0),
  + panel.margin=unit(0,"lines"))
  Error in geom_tallrect(aes(xmin = min/1e+06, xmax = max/1e+06, fill = annotation), :
  could not find function "proto"
  Execution halted
  ** running examples for arch 'x64' ... ERROR
  Running examples in 'bams-Ex.R' failed
  The error most likely occurred in:
  
  > ### Name: neuroblastoma
  > ### Title: Neuroblastoma copy number profiles and breakpoint annotations
  > ### Aliases: neuroblastoma
  > ### Keywords: datasets
  >
  > ### ** Examples
  >
  > data(neuroblastoma)
  > pids <- levels(neuroblastoma$profiles$profile.id)[1:2]
  > pro <- subset(neuroblastoma$profiles,profile.id%in%pids)
  > ann <- subset(neuroblastoma$annotations,profile.id%in%pids)
  > library(ggplot2)
  > ggplot()+
  + geom_tallrect(aes(xmin=min/1e6,xmax=max/1e6,
  + fill=annotation),data=ann)+
  + geom_point(aes(position/1e6,logratio),pch=1,data=pro)+
  + scale_fill_manual(values=c(breakpoint="red",
  + normal="yellow"))+
  + scale_x_continuous(breaks=c(100,200))+
  + facet_grid(profile.id~chromosome,
  + scales="free_x",space="free")+
  + theme_bw()+
  + opts(axis.title.x=theme_text(vjust = 0),
  + panel.margin=unit(0,"lines"))
  Error in geom_tallrect(aes(xmin = min/1e+06, xmax = max/1e+06, fill = annotation), :
  could not find function "proto"
  Execution halted