* using log directory 'd:/Rcompile/CRANpkg/local/2.15/FunNet.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 'FunNet/DESCRIPTION' ... OK
* this is package 'FunNet' version '1.00-12'
* checking package dependencies ... OK
* 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 '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 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
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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
NOTE: There were 3 notes.
See
  'd:/Rcompile/CRANpkg/local/2.15/FunNet.Rcheck/00check.log'
for details.