* using log directory 'd:/Rcompile/CRANpkg/local/3.3/FunCluster.Rcheck'
* using R version 3.3.2 (2016-10-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'FunCluster/DESCRIPTION' ... OK
* this is package 'FunCluster' version '1.09'
* 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 'FunCluster' can be installed ... OK
* checking installed package size ... OK
* 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 use of S3 registration ... OK
* checking 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NB: .First.lib is obsolete and will not be used in R 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 'FunCluster/R/FunCluster.R':
  .First.lib calls:
    cat(paste("\nThis is FunCluster package version ", f.version,     " maintained by Corneliu Henegar.\n\n", "FunCluster(wd='', org='HS', go.direct=FALSE, clusterm='cc', compare='common.correl.genes',\n",     "\tcorr.met='greedy', corr.th=0.85, two.lists=TRUE, restrict=FALSE, alpha=0.05,\n",     "\tlocation=FALSE, details=FALSE)\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'
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'
AnnotationIndirecte: no visible global function definition for
  'write.table'
ChargerKegg: no visible global function definition for 'download.file'
ChargerKegg: no visible global function definition for 'count.fields'
ChargerKegg: no visible global function definition for 'read.table'
ChargerKegg: no visible global function definition for 'write.table'
FunCluster: no visible global function definition for 'read.table'
GeneInfo: no visible global function definition for 'download.file'
GeneInfo: no visible global function definition for 'read.table'
GeneInfoSC: no visible global function definition for 'download.file'
GeneInfoSC: no visible global function definition for 'read.table'
Kegg: no visible global function definition for 'download.file'
Kegg: no visible global function definition for 'read.table'
Kegg: no visible global function definition for 'write.table'
MakeGoHierarchy: no visible global function definition for
  'download.file'
MakeGoHierarchy: no visible global function definition for 'read.table'
MakeGoHierarchy: no visible global function definition for
  'write.table'
MakeGoTerms: no visible global function definition for 'write.table'
MakeLocusNames: no visible global function definition for 'write.table'
MiseEnFormeKegg: no visible global function definition for
  'write.table'
MiseEnFormeKeggSC: no visible global function definition for
  'write.table'
TroisiemeFiltrage: no visible global function definition for
  'write.table'
gene.correl: no visible global function definition for 'as.dist'
gene.correl: no visible global function definition for 'hclust'
gene.correl: no visible global function definition for 'cutree'
goAndLL: no visible global function definition for 'download.file'
goAndLL: no visible global function definition for 'read.table'
pclust: no visible global function definition for 'p.adjust'
pterm: no visible global function definition for 'p.adjust'
pvalues: no visible global function definition for 'fisher.test'
term.compare: no visible global function definition for 'cor.test'
Undefined global functions or variables:
  as.dist cor.test count.fields cutree download.file fisher.test hclust
  p.adjust read.table write.table
Consider adding
  importFrom("stats", "as.dist", "cor.test", "cutree", "fisher.test",
             "hclust", "p.adjust")
  importFrom("utils", "count.fields", "download.file", "read.table",
             "write.table")
to your NAMESPACE file.
* 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 ... [2s] OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE