* using log directory 'd:/Rcompile/CRANpkg/local/2.15/biGraph.Rcheck'
* using R version 2.15.0 (2012-03-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'biGraph/DESCRIPTION' ... OK
* this is package 'biGraph' version '0.9-3'
* checking package dependencies ... NOTE
Package suggested but not available for checking: 'multicore'
* checking if this is a source package ... OK
* checking if there is a namespace ... NOTE
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 whether package 'biGraph' can be installed ... OK
* checking installed package size ... OK
* 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
* 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 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.betweenness.centrality: no visible binding for global
  variable 'type'
bipartite.closeness.centrality: no visible binding for global variable
  'type'
bipartite.projection.informationloss: warning in
  get.incidence(input_graph, type = bipartite$type): partial argument
  match of 'type' to 'types'
bipartite.projection.informationloss: no visible binding for global
  variable 'type'
covLoss: no visible global function definition for 'mclapply'
degree.centrality: no visible binding for global variable 'type'
edge.dH: no visible global function definition for 'mclapply'
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'
graph.dH: no visible global function definition for 'mclapply'
lpi: no visible binding for global variable 'type'
lpi: no visible binding for global variable 'lp'
read.lpi: warning in matrix(elc, nc = 2, byrow = TRUE): partial
  argument match of 'nc' to 'ncol'
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'
vertex.dH: no visible global function definition for 'mclapply'
* 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 ... NOTE
Package(s) unavailable to check Rd xrefs: 'multicore'
* 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... OK
* checking re-building of vignette PDFs ... OK
* checking PDF version of manual ... OK
NOTE: There were 6 notes.
See
  'd:/Rcompile/CRANpkg/local/2.15/biGraph.Rcheck/00check.log'
for details.