diffcorr error

gistfile1.txt

==> R CMD check DiffCorr_0.2.tar.gz

* using log directory ‘/home/kozo2/Documents/DiffCorr.Rcheck’
* using R version 3.1.2 (2014-10-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘DiffCorr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DiffCorr’ version ‘0.2’
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DiffCorr’ 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘fdrtool’ ‘igraph’ ‘pcaMethods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... WARNING
plot:
  function(x, ...)
plot.DiffCorr.group:
  function(data, groups1, groups2, group1.no, group2.no, g1, g2,
           g1.order, g2.order, title1, title2, ...)

plot:
  function(x, ...)
plot.cluster.molecules:
  function(data, groups, group.no, title, ylim, order, scale.center,
           scale.scale, frame, col, bottom.mar, xlab, ylab)

See section ‘Generic functions and methods’ of the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cluster.molecule: warning in cor.dist(data, method = methods, absolut =
  abs): partial argument match of 'method' to 'methods'
cluster.molecule: warning in cor.dist(data, method = methods, absolut =
  abs): partial argument match of 'absolut' to 'absolute'
cor2.test: warning in pt(t, df, lower = FALSE): partial argument match
  of 'lower' to 'lower.tail'
cor2.test: warning in pnorm(z, lower = FALSE): partial argument match
  of 'lower' to 'lower.tail'
plot.DiffCorr.group: warning in plot.cluster.molecules(d = g1.data,
  order = g1.order, title = title1, ...): partial argument match of 'd'
  to 'data'
plot.DiffCorr.group: warning in plot.cluster.molecules(d = g2.data,
  order = g2.order, title = title2, ...): partial argument match of 'd'
  to 'data'
plot.DiffCorr.group: warning in close.screen(all = TRUE): partial
  argument match of 'all' to 'all.screens'
generate_g: no visible global function definition for ‘simplify’
generate_g: no visible global function definition for ‘graph.adjacency’
generate_g: no visible global function definition for ‘V’
generate_g: no visible global function definition for ‘V<-’
generate_g: no visible global function definition for ‘E’
generate_g: no visible global function definition for ‘E<-’
get.eigen.molecule: no visible global function definition for ‘pca’
get.lfdr: no visible global function definition for ‘fdrtool’
* 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 ... WARNING
Undocumented arguments in documentation object 'cluster.molecule'
  ‘methods’ ‘abs’
Documented arguments not in \usage in documentation object 'cluster.molecule':
  ‘method’

Documented arguments not in \usage in documentation object 'comp.2.cc.fdr':
  ‘r’

Undocumented arguments in documentation object 'get.eigen.molecule'
  ‘groups’ ‘methods’ ‘n’
Documented arguments not in \usage in documentation object 'get.eigen.molecule':
  ‘sc’

Undocumented arguments in documentation object 'plot.DiffCorr.group'
  ‘group1.no’ ‘group2.no’ ‘...’
Documented arguments not in \usage in documentation object 'plot.DiffCorr.group':
  ‘groups1.no’ ‘groups2.no’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object 'plot.DiffCorr.group':
  ‘plot.DiffCorr.group’

S3 methods shown with full name in documentation object 'plot.cluster.molecules':
  ‘plot.cluster.molecules’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... WARNING
Argument items with no description in Rd object 'get.eigen.molecule':
  ‘whichgroups’

Argument items with no description in Rd object 'plot.cluster.molecules':
  ‘groups’ ‘group.no’

* checking for unstated dependencies in examples ... WARNING
'data(package=)' call not declared from: ‘multtest’
* checking examples ... ERROR
Running examples in ‘DiffCorr-Ex.R’ failed
The error most likely occurred in:

> ### Name: comp.2.cc.fdr
> ### Title: Export differential correlations between two conditions
> ### Aliases: comp.2.cc.fdr
> 
> ### ** Examples
> 
> library(fdrtool)
> data(golub, package = "multtest")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘multtest’
Calls: data -> find.package
Execution halted

Exited with status 1.