• using R version 2.10.1 Patched (2010-02-06 r51106)
• using session charset: UTF-8
• checking for file 'clusterfly/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'clusterfly' version '0.2.2'
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking whether package 'clusterfly' can be installed ... 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 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
  addhull: no visible global function definition for ‘setEdges’
  cfly_dist: no visible binding for global variable ‘value’
  qhull: no visible binding for global variable ‘i’
  qhull: no visible binding for global variable ‘j’
  xtable.table: no visible global function definition for ‘xtable.matrix’
• checking Rd files ... WARNING
  prepare_Rd: addhull-yt.rd:21: Dropping empty section \examples
  prepare_Rd: as-data-frame-clusterfly-2y.rd:15: Dropping empty section \details
  prepare_Rd: as-data-frame-clusterfly-2y.rd:17: Dropping empty section \examples
  prepare_Rd: cfly-fluct-a9.rd:18: Dropping empty section \details
  prepare_Rd: cfly-pcp-ax.rd:19: Dropping empty section \examples
  prepare_Rd: cfly-show-7h.rd:16: Dropping empty section \details
  prepare_Rd: cfly-show-7h.rd:18: Dropping empty section \examples
  prepare_Rd: clarify-c0.rd:16: Dropping empty section \details
  prepare_Rd: clarify-c0.rd:18: Dropping empty section \examples
  prepare_Rd: clusterfly-yt.rd:29: Dropping empty section \examples
  prepare_Rd: clusters-ap.rd:16: Dropping empty section \details
  prepare_Rd: clusters-ap.rd:18: Dropping empty section \examples
  prepare_Rd: combinerows-1k.rd:15: Dropping empty section \details
  prepare_Rd: combinerows-1k.rd:17: Dropping empty section \examples
  prepare_Rd: cut-hierfly-ey.rd:17: Dropping empty section \details
  prepare_Rd: ellipse-e8.rd:24: Dropping empty section \examples
  prepare_Rd: get--set--clusterfly-r9.rd:6-8: Dropping empty section \description
  prepare_Rd: get--set--clusterfly-r9.rd:16: Dropping empty section \details
  prepare_Rd: get--set--clusterfly-r9.rd:18: Dropping empty section \examples
  checkRd: (7) file 'get--set--clusterfly-r9.rd': Must have a \description
  prepare_Rd: hierarchical-1f.rd:17: Dropping empty section \details
  prepare_Rd: hierarchical-1f.rd:19: Dropping empty section \examples
  prepare_Rd: make-net-7n.rd:15: Dropping empty section \details
  prepare_Rd: make-net-7n.rd:17: Dropping empty section \examples
  prepare_Rd: mefly-r7.rd:15: Dropping empty section \details
  prepare_Rd: o.rd:5-7: Dropping empty section \description
  prepare_Rd: o.rd:9: Dropping empty section \format
  checkRd: (7) file 'o.rd': Must have a \description
  prepare_Rd: print-clusterfly-dk.rd:15: Dropping empty section \details
  prepare_Rd: print-clusterfly-dk.rd:17: Dropping empty section \examples
  prepare_Rd: print-hierfly-89.rd:15: Dropping empty section \details
  prepare_Rd: print-hierfly-89.rd:17: Dropping empty section \examples
  prepare_Rd: qhull-1v.rd:14: Dropping empty section \details
  prepare_Rd: qhull-1v.rd:16: Dropping empty section \examples
  prepare_Rd: qhullout-jl.rd:14: Dropping empty section \details
  prepare_Rd: qhullout-jl.rd:16: Dropping empty section \examples
  prepare_Rd: xtable-table-7n.rd:15: Dropping empty section \details
  prepare_Rd: xtable-table-7n.rd:17: Dropping empty section \examples
• checking Rd metadata ... OK
• checking Rd cross-references ... WARNING
  Unknown package(s) ‘ggplot’ in Rd xrefs
• 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 'as.data.frame.clusterfly':
  as.data.frame.clusterfly
  
  S3 methods shown with full name in documentation object 'cut.hierfly':
  cut.hierfly
  
  S3 methods shown with full name in documentation object '"[[<-.clusterfly"':
  [[<-.clusterfly
  
  S3 methods shown with full name in documentation object 'ggobi.hierfly':
  ggobi.hierfly
  
  S3 methods shown with full name in documentation object 'ggobi.som':
  ggobi.som
  
  S3 methods shown with full name in documentation object 'print.clusterfly':
  print.clusterfly
  
  S3 methods shown with full name in documentation object 'print.hierfly':
  print.hierfly
  
  The \usage entries for S3 methods should use the \method markup and not
  their full name.
  See the chapter 'Writing R documentation files' in manual 'Writing R
  Extensions'.
• checking data for non-ASCII characters ... OK
• checking examples ... OK
• checking PDF version of manual ... OK