• using R Under development (unstable) (2012-05-19 r59366)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘biGraph/DESCRIPTION’ ... OK
• this is package ‘biGraph’ version ‘0.9-3’
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... WARNING
  As from R 2.14.0 all packages need a namespace.
  One will be generated on installation, but it is better to handcraft a
  NAMESPACE file: R CMD build will produce a suitable starting point.
  CRAN requires a NAMESPACE file for all submissions.
• checking for executable files ... OK
• checking whether package ‘biGraph’ 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 loading without being on the library search path ... 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
  bipartite.projection.informationloss: warning in
  get.incidence(input_graph, type = bipartite$type): partial argument
  match of 'type' to 'types'
  read.lpi: warning in matrix(elc, nc = 2, byrow = TRUE): partial
  argument match of 'nc' to 'ncol'
  bipartite.betweenness.centrality: no visible binding for global
  variable ‘type’
  bipartite.closeness.centrality: no visible binding for global variable
  ‘type’
  bipartite.projection.informationloss: no visible binding for global
  variable ‘type’
  degree.centrality: no visible binding for global variable ‘type’
  edge.dH: no visible binding for global variable ‘H.after’
  get.Hafter.edge: no visible global function definition for ‘nei’
  get.Hafter.edge: no visible binding for global variable ‘id’
  get.Hafter.vertex: no visible binding for global variable ‘id’
  get.weighted.projection: no visible binding for global variable ‘type’
  lpi: no visible binding for global variable ‘type’
  lpi: no visible binding for global variable ‘lp’
  single.mode.betweenness.centralization: no visible binding for global
  variable ‘type’
  single.mode.closeness.centralization: no visible binding for global
  variable ‘type’
  single.mode.degree.centralization: no visible binding for global
  variable ‘type’
  vertex.avCovLoss: no visible global function definition for ‘to’
• checking Rd files ... NOTE
  prepare_Rd: biGraph-internal.Rd:32-33: Dropping empty section \examples
  prepare_Rd: bipartite.closeness.centrality.Rd:33-34: Dropping empty section \note
  prepare_Rd: bipartite.graph.density.Rd:33-34: Dropping empty section \note
  prepare_Rd: bipartite.projection.informationloss.Rd:64-66: Dropping empty section \note
  prepare_Rd: degree.centrality.Rd:37-38: Dropping empty section \note
  prepare_Rd: g.Rd:20-21: Dropping empty section \references
  prepare_Rd: lpi.Rd:42-44: Dropping empty section \note
  prepare_Rd: print.lpi.Rd:22-24: Dropping empty section \details
  prepare_Rd: print.lpi.Rd:25-31: Dropping empty section \value
  prepare_Rd: print.lpi.Rd:38-40: Dropping empty section \note
  prepare_Rd: print.lpi.Rd:44-46: Dropping empty section \seealso
  prepare_Rd: print.summary.lpi.Rd:22-24: Dropping empty section \details
  prepare_Rd: print.summary.lpi.Rd:25-31: Dropping empty section \value
  prepare_Rd: print.summary.lpi.Rd:38-40: Dropping empty section \note
  prepare_Rd: read.lpi.Rd:25-26: Dropping empty section \details
  prepare_Rd: read.lpi.Rd:38-40: Dropping empty section \note
  prepare_Rd: single.mode.closeness.centralization.Rd:34-35: Dropping empty section \note
  prepare_Rd: single.mode.degree.centralization.Rd:33-34: Dropping empty section \note
  prepare_Rd: summary.lpi.Rd:22-24: Dropping empty section \details
  prepare_Rd: summary.lpi.Rd:38-40: Dropping empty section \note
  prepare_Rd: write.lpi.Rd:22-24: Dropping empty section \details
  prepare_Rd: write.lpi.Rd:25-26: Dropping empty section \value
  prepare_Rd: write.lpi.Rd:33-35: Dropping empty section \note
• 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’ ... NOTE
  The following files are already in R: ‘Sweave.sty’
  Please remove them from your package.
  The following files should probably not be installed:
  ‘authblk.sty’, ‘fullpage.sty’, ‘pnas2010.bst’
  
  Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
  or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
• checking examples ... [3s/3s] OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... [2s/2s] OK
• checking re-building of vignette PDFs ... [3s/4s] OK
• checking PDF version of manual ... OK
  WARNING: There was 1 warning.
  NOTE: There were 3 notes.
  See
  ‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/biGraph.Rcheck/00check.log’
  for details.