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fftrees log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2014-11-17-17-05/RF_PKG_CHECK/PKGS/fftrees.Rcheck'
* using R version 3.1.2 Patched (2014-11-14 r66984)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'fftrees/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'fftrees' version '1.0.4'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Marc Giesmann '
New submission
Uses the superseded package: 'doSNOW (>= 1.0.0)'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
  No repository set, so cyclic dependency check skipped
* 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 'fftrees' can be installed ... WARNING
Found the following significant warnings:
  Warning: R:/run/building/build_2014-11-17-17-05/RF_PKG_CHECK/PKGS/fftrees.Rcheck/00_pkg_src/fftrees/man/FFTEST-package.Rd:30: All text must be in a section
  Warning: R:/run/building/build_2014-11-17-17-05/RF_PKG_CHECK/PKGS/fftrees.Rcheck/00_pkg_src/fftrees/man/FFTEST-package.Rd:31: All text must be in a section
See 'R:/run/building/build_2014-11-17-17-05/RF_PKG_CHECK/PKGS/fftrees.Rcheck/00install.out' for details.
* 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
* 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
** 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
* 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 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
Note: no visible binding for global variable '.Data' 
Note: no visible binding for global variable 'criterion' 
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... WARNING
Sdt:
  function(hi, ...)
Sdt.default:
  function(hi, fa, mi, cr)

Sdt:
  function(hi, ...)
Sdt.fftree:
  function(tree)

Sdt:
  function(hi, ...)
Sdt.logical:
  function(criterion, prediction)

prune:
  function(x, ...)
prune.fftree:
  function(tree, n)

plot:
  function(x, ...)
plot.fftree:
  function(object, ...)

See section 'Generic functions and methods' of the 'Writing R
Extensions' manual.
* checking replacement functions ... WARNING
Note: no visible binding for global variable '.Data' 
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... NOTE
Note: no visible binding for global variable '.Data' 
Note: no visible binding for global variable 'criterion' 
See the chapter 'System and foreign language interfaces' of the
'Writing R Extensions' manual.
* checking R code for possible problems ... NOTE
Note: no visible binding for global variable '.Data' 
File 'fftrees/R/misc.R':
  .onLoad calls:
    require(compiler)
    packageStartupMessage("Package 'compiler' found and activated. Ignore notes about missing 'visible binding for global variable'.")
    packageStartupMessage("Package 'compiler' isn't installed. For huge performance boost install it, and reload ",     pkgname, ".")

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.

Note: no visible binding for global variable '.Data' 
Note: no visible binding for global variable '.Data' 
Note: no visible binding for global variable '.Data' 
Note: no visible binding for global variable 'criterion' 
fftm.montecarlo: no visible global function definition for
  'makeCluster'
fftm.montecarlo: no visible global function definition for
  'clusterCall'
fftm.montecarlo: no visible global function definition for
  'stopCluster'
permu.new: no visible global function definition for 'makeCluster'
permu.new: no visible global function definition for 'stopCluster'
splitvalanalysis: no visible binding for global variable 'rawdata'

Found the following assignments to the global environment:
File 'fftrees/R/misc.R':
  assign(variable, NULL, envir = .GlobalEnv)

Found the following calls to data() loading into the global environment:
File 'fftrees/R/misc.R':
  data(Titanic)
  data(UCBAdmissions)
See section 'Good practice' in '?data'.
* checking Rd files ... WARNING
prepare_Rd: FFTEST-package.Rd:30: All text must be in a section
prepare_Rd: FFTEST-package.Rd:31: All text must be in a section
prepare_Rd: FFTEST-package.Rd:37-39: Dropping empty section \examples
Fftm.Rd: non-ASCII input and no declared encoding
problem found in 'Fftm.Rd'
* checking Rd metadata ... WARNING
Rd files with duplicated alias 'as.data.frame':
  'as.data.frame-cue-method.Rd' 'as.data.frame-fftree-method.Rd'
* checking Rd line widths ... NOTE
Rd file 'chase.Rd':
  \examples lines wider than 100 characters:
     tree <- Fftm(Survived ~ Age, "chase",rawdata, whatToMaximize = "percCorr", chaseHow = "max", forward=TRUE)
     tree2 <- Fftm(Survived ~ Age, "chase",rawdata, whatToMaximize = c("percCorr","dPr"), chaseHow = c("max","min"), forward=c(TRUE,FALSE))

Rd file 'montecarlo.Rd':
  \examples lines wider than 100 characters:
     tree <- Fftm(Survived ~ Age + Sex + Class, "montecarlo",rawdata, whatToMaximize = "percCorr", blocksize = 1000, threshold=.001, cores=4 ... [TRUNCATED]

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... WARNING
Unknown package '' in Rd xrefs
* checking for missing documentation entries ... WARNING
Note: no visible binding for global variable '.Data' 
Undocumented S4 methods:
  generic 'predict' and siglist 'cue'
  generic 'update' and siglist 'fftree'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Note: no visible binding for global variable '.Data' 
Note: no visible binding for global variable 'criterion' 
Codoc mismatches from documentation object 'plot':
plot.fftree
  Code: function(object, ...)
  Docs: function(object, showBoldness = FALSE, ...)
  Argument names in docs not in code:
    showBoldness
  Mismatches in argument names:
    Position: 2 Code: ... Docs: showBoldness

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'predict,fftree-method'
  '...'

Objects in \usage without \alias in documentation object 'predict':
  '\S4method{predict}{cue}'

Undocumented arguments in documentation object 'show'
  'object'
Objects in \usage without \alias in documentation object 'show':
  '\S4method{show}{cue}' '\S4method{show}{fftree}'

Documented arguments not in \usage in documentation object 'toString,cue-method':
  'object'

Objects in \usage without \alias in documentation object 'update':
  '\S4method{update}{fftree}'

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.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
maximize   1.73   0.73   19.94
montecarlo 0.32   0.28    6.11
permu.new  0.40   0.04    7.11
** running examples for arch 'x64' ...Warning in file(con, "r") :
  cannot open file '../fftrees-Ex_x64.Rout': Permission denied
Error in file(con, "r") : cannot open the connection
Execution halted
Run time: 236.11 seconds.