• using R version 2.10.0 Patched (2009-11-05 r50317)
• using session charset: UTF-8
• checking for file 'graph/DESCRIPTION' ... OK
• this is package 'graph' version '1.22.2'
• checking package name space information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking whether package 'graph' can be installed ... WARNING
  Found the following significant warnings:
  Warning: ./man/renderInfo-class.Rd:115: unknown macro '\textit'
  See http://www.r-project.org/nosvn/R.check/r-patched-linux-x86_64/graph-00install.html for details.
• 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 name space 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
  inEdges,character-graphNEL: no visible binding for global variable
  ‘from’
• checking Rd files ... WARNING
  prepare_Rd: graphRendering.Rd:21: Dropping empty section \keyword
  prepare_Rd: graphRendering.Rd:10-12: Dropping empty section \details
  prepare_Rd: graphRendering.Rd:14-16: Dropping empty section \seealso
  prepare_Rd: graphRendering.Rd:18-20: Dropping empty section \examples
  prepare_Rd: leaves.Rd:41: Dropping empty section \keyword
  prepare_Rd: renderInfo-class.Rd:115: unknown macro '\textit'
• checking Rd metadata ... OK
• checking Rd cross-references ... WARNING
  Unknown package(s) ‘Graphviz’ in Rd xrefs
  Missing link(s) in documentation object './man/fromGXL-methods.Rd':
  ‘[graph]{graphNEL}’
  
  See the information in section 'Cross-references' of the 'Writing R
  Extensions' manual.
  
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... WARNING
  Codoc mismatches from documentation object 'combineNodes':
  \S4method{combineNodes}{character,graphNEL,character}
  Code: function(nodes, graph, newName, collapseFunction = sum)
  Docs: function(nodes, graph, newName, collapseFun = sum)
  Argument names in code not in docs:
  collapseFunction
  Argument names in docs not in code:
  collapseFun
  Mismatches in argument names:
  Position: 4 Code: collapseFunction Docs: collapseFun
  
  Codoc mismatches from documentation object 'Coercions between matrix and graph representations':
  \S4method{coerce}{graphNEL,matrix}
  Code: function(from, to = "matrix", strict = TRUE)
  Docs: function(g, m)
  Argument names in code not in docs:
  from to strict
  Argument names in docs not in code:
  g m
  Mismatches in argument names:
  Position: 1 Code: from Docs: g
  Position: 2 Code: to Docs: m
  \S4method{coerce}{matrix,graphNEL}
  Code: function(from, to = "graphNEL", strict = TRUE)
  Docs: function(m, g)
  Argument names in code not in docs:
  from to strict
  Argument names in docs not in code:
  m g
  Mismatches in argument names:
  Position: 1 Code: from Docs: m
  Position: 2 Code: to Docs: g
  
  S4 class codoc mismatches from documentation object 'graph-class':
  Slots for class 'graph'
  Code: edgeData graphData nodeData renderInfo
  Docs: edgeData graphData nodeData
  
  S4 class codoc mismatches from documentation object 'graphAM-class':
  Slots for class 'graphAM'
  Code: adjMat edgeData graphData nodeData renderInfo
  Inherited: edgeData nodeData renderInfo graphData
  Docs: adjMat edgeData edgemode nodeData
  
• checking Rd \usage sections ... OK
• checking data for non-ASCII characters ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking for portable compilation flags in Makevars ... OK
• checking for portable use of $BLAS_LIBS ... OK
• checking examples ... OK
• checking package vignettes in 'inst/doc' ... OK
• checking PDF version of manual ... OK