• using R version 3.0.1 (2013-05-16)
• using platform: x86_64-w64-mingw32 (64-bit)
• using session charset: ISO8859-1
• checking for file 'FunNet/DESCRIPTION' ... OK
• this is package 'FunNet' version '1.00-12'
• 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 for hidden files and directories ... OK
• checking for portable file names ... OK
• checking whether package 'FunNet' can be installed ... OK
• checking installed package size ... NOTE
  installed size is 6.5Mb
  sub-directories of 1Mb or more:
  R 5.0Mb
  data 1.4Mb
• checking package directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over 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 whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace 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
  NB: .First.lib is obsolete and will not be used in R >= 3.0.0
  File 'FunNet/R/FunNet.R':
  .First.lib calls:
  cat(paste("\nThis is FunNet package ", .funnet.version, " built and maintained by Corneliu Henegar.\n", "Using Gene Ontology and KEGG annotations updated on ", annot.date, ".\n\n", "FunNet(wd='', org=c('hsa','mmu','rno','sce','gga','ath','dre','cel','dme'), two.lists=TRUE, up.frame=NULL,\n", "\t genes.frame=NULL, restrict=FALSE, ref.list=NULL, logged=FALSE,\n", "\t down.frame=NULL, discriminant=FALSE, go.bp=TRUE, go.cc=TRUE, go.mf=TRUE,\n", "\t kegg=TRUE, annot.method=c('specificity','terminological','decorrelated'),\n", "\t annot.details=TRUE, direct=FALSE, enriched=TRUE, fdr=5, build.annot.net=TRUE,\n", "\t coexp.matrix=NULL, coexp.method=c('spearman','pearson','kendall','euclid'),\n", "\t estimate.th=FALSE, hard.th=NA, soft.th=NA, topological = FALSE, keep.sign=FALSE,\n", "\t level=NA, annot.clust.method=c('umilds','ucknn'), annot.prox.measure=c('dynamical',\n", "\t 'unilat.pond.norm.mean','unilat.norm.sum','norm.sum','pond.norm.mean'),\n", "\t test.recovery=FALSE, test.robust=FALSE, replace.annot=NA,random.annot=FALSE,\n", "\t build.gene.net=FALSE, gene.clust.method='hclust', gene.net.details=FALSE,\n", "\t gene.clusters=NA, alpha=0.05, RV=0.90, sigma=NA, keep.rdata=FALSE, zip=TRUE)\n\n", sep = ""))
  
  Package startup functions should use 'packageStartupMessage' to
  generate messages.
  See section 'Good practice' in '?.onAttach'.
  
  .MiseEnFormeKegg: warning in gl(1, NbKmap, label = LL): partial
  argument match of 'label' to 'labels'
  .MiseEnFormeKeggSC: warning in gl(1, NbKmap, label = LL): partial
  argument match of 'label' to 'labels'
  .central.plot.one: warning in CairoPNG(file = paste(extra, taxoname, "
  Centrality.png", sep = ""), height = height, width = width, res =
  600): partial argument match of 'file' to 'filename'
  .central.plot.two: warning in CairoPNG(file = paste(extra, taxoname, "
  Centrality.png", sep = ""), height = height, width = width, res =
  600): partial argument match of 'file' to 'filename'
  .compute.global.distances: warning in
  dudi.pca(as.matrix(marker.matrix[[i]][, match(theme.mask,
  colnames(marker.matrix[[i]]))]), scale = TRUE, scan = FALSE): partial
  argument match of 'scan' to 'scannf'
  .compute.global.distances: warning in
  dudi.pca(as.matrix(marker.matrix[[i + 1]][, match(theme.mask,
  colnames(marker.matrix[[i + 1]]))]), scale = TRUE, scan = FALSE):
  partial argument match of 'scan' to 'scannf'
  .compute.global.distances: warning in coinertia(dudi1, dudi2, scan =
  FALSE, nf = 2): partial argument match of 'scan' to 'scannf'
  .dynamic.proximity: warning in coinertia(xt, xtt, scan = FALSE, nf =
  ncol(marker.matrix[[steps]])): partial argument match of 'scan' to
  'scannf'
  .pcor.mat: warning in cov(xdata, xdata, m = method): partial argument
  match of 'm' to 'method'
  .pcor.mat: warning in cov(xdata, zdata, m = method): partial argument
  match of 'm' to 'method'
  .pcor.mat: warning in cov(zdata, zdata, m = method): partial argument
  match of 'm' to 'method'
  .pcor.rec: warning in cor(tdata[, 1], tdata[, 2], m = method): partial
  argument match of 'm' to 'method'
  .profil.plot.one: warning in CairoPNG(file = paste(extra, taxoname, "
  Level ", i, ".png", sep = ""), height = 0.85 * height, width = 0.85 *
  width, res = 600): partial argument match of 'file' to 'filename'
  .profil.plot.one: warning in CairoPNG(file = paste(extra, taxoname,
  ".png", sep = ""), height = 0.85 * height, width = 0.85 * width, res
  = 600): partial argument match of 'file' to 'filename'
  .profil.plot.two: warning in CairoPNG(file = paste(extra, taxoname, "
  Level ", i, ".png", sep = ""), height = 0.85 * height, width = 0.85 *
  width, res = 600): partial argument match of 'file' to 'filename'
  .profil.plot.two: warning in CairoPNG(file = paste(extra, taxoname,
  ".png", sep = ""), height = 0.85 * height, width = 0.85 * width, res
  = 600): partial argument match of 'file' to 'filename'
  .prop.alt: warning in matrix(seq(from = adjustment.args$edf.lower, by =
  stepsize, len = adjustment.args$num.steps), nr =
  adjustment.args$num.steps, nc = 1): partial argument match of 'nr' to
  'nrow'
  .prop.alt: warning in matrix(seq(from = adjustment.args$edf.lower, by =
  stepsize, len = adjustment.args$num.steps), nr =
  adjustment.args$num.steps, nc = 1): partial argument match of 'nc' to
  'ncol'
• 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 R/sysdata.rda ... OK
• checking examples ... OK
• checking PDF version of manual ... OK
  NOTE: There were 2 notes.
  See
  'd:/Rcompile/CRANpkg/local/3.0/FunNet.Rcheck/00check.log'
  for details.