* using log directory 'd:/Rcompile/CRANpkg/local/2.15/snpXpert.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 'snpXpert/DESCRIPTION' ... OK
* this is package 'snpXpert' version '1.0'
* 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 'snpXpert' can be installed ... OK
* checking installed package size ... OK
* 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
snpXpert: no visible binding for '<<-' assignment to 'Result.tt'
snpXpert: no visible binding for global variable 'Result.tt'
snpXpert : <anonymous>: no visible binding for global variable
  'Result.tt'
snpXpert : <anonymous>: no visible binding for global variable
  'SNPlist.id'
snpXpert : <anonymous>: no visible binding for global variable
  'Class.data'
snpXpert: no visible binding for '<<-' assignment to 'tn'
snpXpert: no visible binding for global variable 'tn'
snpXpert : readF: no visible binding for '<<-' assignment to 'RAW.data'
snpXpert : selectClass: no visible binding for '<<-' assignment to
  'list.name'
snpXpert : selectClass: no visible binding for global variable
  'RAW.data'
snpXpert : selectClass: no visible binding for global variable
  'list.name'
snpXpert : selectClass : OnOK: no visible binding for '<<-' assignment
  to 'classID'
snpXpert : selectClass : OnOK: no visible binding for global variable
  'list.name'
snpXpert : selectSNPs: no visible binding for '<<-' assignment to
  'list.name'
snpXpert : selectSNPs: no visible binding for global variable
  'RAW.data'
snpXpert : selectSNPs: no visible binding for global variable
  'list.name'
snpXpert : selectSNPs : OnOK: no visible binding for global variable
  'list.name'
snpXpert : selectSNPs : OnOK: no visible binding for '<<-' assignment
  to 'SNPlist.id'
snpXpert : genotypeDialog: no visible binding for global variable
  'RAW.data'
snpXpert : genotypeDialog: no visible binding for '<<-' assignment to
  'SNP.table'
snpXpert : genotypeDialog: no visible binding for global variable
  'SNP.table'
snpXpert : genotypeDialog: no visible binding for '<<-' assignment to
  'ReturnVal'
snpXpert : genotypeDialog : onOK: no visible binding for global
  variable 'SNP.table'
snpXpert : genotypeDialog : onOK: no visible binding for '<<-'
  assignment to 'ReturnVal'
snpXpert : genotypeDialog : onOK: no visible binding for global
  variable 'ReturnVal'
snpXpert : genotypeDialog : onCancel: no visible binding for '<<-'
  assignment to 'ReturnVal'
snpXpert : genotypeDialog: no visible binding for global variable
  'ReturnVal'
snpXpert : dataType: no visible binding for global variable 'RAW.data'
snpXpert : makeForm.data: no visible binding for '<<-' assignment to
  'Form.data'
snpXpert : makeForm.data: no visible binding for global variable
  'RAW.data'
snpXpert : makeForm.data: no visible binding for global variable
  'Form.data'
snpXpert : CaseControl.set: no visible binding for global variable
  'Form.data'
snpXpert : CaseControl.set: no visible binding for global variable
  'classID'
snpXpert : CaseControl.set : OnOK: no visible binding for '<<-'
  assignment to 'cbVal.case'
snpXpert : CaseControl.set : OnOK: no visible binding for '<<-'
  assignment to 'cbVal.control'
snpXpert : CaseControl.set : OnOK: no visible binding for global
  variable 'Form.data'
snpXpert : CaseControl.set : OnOK: no visible binding for global
  variable 'classID'
snpXpert : CaseControl.set : OnOK: no visible binding for global
  variable 'cbVal.case'
snpXpert : CaseControl.set : OnOK: no visible binding for global
  variable 'cbVal.control'
snpXpert : CaseControl.set : OnOK: no visible binding for '<<-'
  assignment to 'control.id'
snpXpert : CaseControl.set : OnOK: no visible binding for global
  variable 'control.id'
snpXpert : CaseControl.set : OnOK: no visible binding for '<<-'
  assignment to 'case.id'
snpXpert : CaseControl.set : OnOK: no visible binding for global
  variable 'case.id'
snpXpert : CaseControl.set : OnOK: no visible binding for '<<-'
  assignment to 'test.selected.id'
snpXpert : CaseControl.set : OnOK: no visible binding for '<<-'
  assignment to 'Class.data'
snpXpert : CaseControl.set : OnOK: no visible binding for global
  variable 'Class.data'
snpXpert : HWE: no visible binding for global variable 'Form.data'
snpXpert : HWE: no visible binding for '<<-' assignment to 'HWE.result'
snpXpert : HWE: no visible binding for global variable 'classID'
snpXpert : HWE: no visible binding for global variable 'HWE.result'
snpXpert : add.tab.list: no visible binding for global variable 'tn'
snpXpert : chiX2.allele.test: no visible binding for global variable
  'Form.data'
snpXpert : chiX2.allele.test: no visible binding for '<<-' assignment
  to 'chiX2.allele.result'
snpXpert : chiX2.allele.test: no visible binding for global variable
  'classID'
snpXpert : chiX2.allele.test: no visible binding for global variable
  'chiX2.allele.result'
snpXpert : chiX2.genotype.test: no visible binding for global variable
  'Form.data'
snpXpert : chiX2.genotype.test: warning in factor(apply(hap, 1,
  function(x) {: partial argument match of 'level' to 'levels'
snpXpert : chiX2.genotype.test: warning in sum(x ==
  names(temp.table1)[sort.id[2]]): partial argument match of 'level' to
  'levels'
snpXpert : chiX2.genotype.test: warning in }), level = c(0, 1, 2)):
  partial argument match of 'level' to 'levels'
snpXpert : chiX2.genotype.test: no visible binding for '<<-' assignment
  to 'chiX2.genotype.result'
snpXpert : chiX2.genotype.test: no visible binding for global variable
  'classID'
snpXpert : chiX2.genotype.test: no visible binding for global variable
  'chiX2.genotype.result'
snpXpert : regression.test: no visible binding for '<<-' assignment to
  'Cov.id'
snpXpert : regression.test: no visible binding for '<<-' assignment to
  'list.name'
snpXpert : regression.test: no visible binding for global variable
  'RAW.data'
snpXpert : regression.test: no visible binding for global variable
  'list.name'
snpXpert : regression.test : OnOK1: no visible binding for '<<-'
  assignment to 'Y.id'
snpXpert : regression.test : OnOK1: no visible binding for global
  variable 'RAW.data'
snpXpert : regression.test : OnOK1: no visible binding for '<<-'
  assignment to 'list.name'
snpXpert : regression.test : OnOK1: no visible binding for global
  variable 'list.name'
snpXpert : regression.test : OnOK1 : OnOK2: no visible binding for
  '<<-' assignment to 'SNPlist.id.test'
snpXpert : regression.test : OnOK1 : OnOK2: no visible binding for
  global variable 'RAW.data'
snpXpert : regression.test : OnOK1 : OnOK2: no visible binding for
  global variable 'SNPlist.id.test'
snpXpert : regression.test : OnOK1 : OnOK2 : OnOK3: no visible binding
  for '<<-' assignment to 'SNPMode'
snpXpert : regression.test : OnOK1 : OnOK2 : OnOK3: no visible binding
  for global variable 'SNPMode'
snpXpert : regression.test : OnOK1 : OnOK2 : OnOK3: no visible binding
  for global variable 'RAW.data'
snpXpert : regression.test : OnOK1 : OnOK2 : OnOK3: no visible binding
  for global variable 'classID'
snpXpert : regression.test : OnOK1 : OnOK2 : OnOK3: no visible binding
  for global variable 'Y.id'
snpXpert : regression.test : OnOK1 : OnOK2 : OnOK3 : OnOK4: no visible
  binding for '<<-' assignment to 'Cov.id'
snpXpert : regression.test : OnOK1 : OnOK2 : OnOK3 : OnOK4: no visible
  binding for global variable 'RAW.data'
snpXpert : regression.test : OnOK1 : OnOK2 : OnOK3 : OnOK4: no visible
  binding for global variable 'classID'
snpXpert : regression.test : OnOK1 : OnOK2 : OnOK3 : OnOK4: no visible
  binding for global variable 'Y.id'
snpXpert : regression.test : OnOK1 : OnOK2 : OnOK3 : OnOK4: no visible
  binding for global variable 'Form.data'
snpXpert : regression.test : OnOK1 : OnOK2 : OnOK3 : OnOK4: no visible
  binding for global variable 'SNPlist.id.test'
snpXpert : regression.test : OnOK1 : OnOK2 : OnOK3 : OnOK4: no visible
  binding for global variable 'SNPMode'
snpXpert : regression.test : OnOK1 : OnOK2 : OnOK3 : OnOK4: no visible
  binding for global variable 'Cov.id'
snpXpert : regression.test : OnOK1 : OnOK2 : OnOK3 : OnOK4: no visible
  binding for '<<-' assignment to 'REG.summary'
snpXpert : regression.test : OnOK1 : OnOK2 : OnOK3 : OnOK4: no visible
  binding for global variable 'REG.summary'
snpXpert : logistic.test: no visible binding for '<<-' assignment to
  'Cov.id'
snpXpert : logistic.test: no visible binding for '<<-' assignment to
  'list.name'
snpXpert : logistic.test: no visible binding for global variable
  'RAW.data'
snpXpert : logistic.test: no visible binding for global variable
  'list.name'
snpXpert : logistic.test : OnOK1: no visible binding for global
  variable 'list.name'
snpXpert : logistic.test : OnOK1: no visible binding for '<<-'
  assignment to 'SNPlist.id.test'
snpXpert : logistic.test : OnOK1: no visible binding for global
  variable 'RAW.data'
snpXpert : logistic.test : OnOK1: no visible binding for global
  variable 'SNPlist.id.test'
snpXpert : logistic.test : OnOK1: no visible binding for '<<-'
  assignment to 'list.name'
snpXpert : logistic.test : OnOK1 : OnOK2: no visible binding for '<<-'
  assignment to 'SNPMode'
snpXpert : logistic.test : OnOK1 : OnOK2: no visible binding for global
  variable 'RAW.data'
snpXpert : logistic.test : OnOK1 : OnOK2: no visible binding for global
  variable 'SNPlist.id.test'
snpXpert : logistic.test : OnOK1 : OnOK2: no visible binding for global
  variable 'SNPMode'
snpXpert : logistic.test : OnOK1 : OnOK2: no visible binding for global
  variable 'list.name'
snpXpert : logistic.test : OnOK1 : OnOK2: no visible binding for '<<-'
  assignment to 'list.name'
snpXpert : logistic.test : OnOK1 : OnOK2: no visible binding for global
  variable 'classID'
snpXpert : logistic.test : OnOK1 : OnOK2 : OnOK3: no visible binding
  for global variable 'list.name'
snpXpert : logistic.test : OnOK1 : OnOK2 : OnOK3: no visible binding
  for '<<-' assignment to 'Cov.id'
snpXpert : logistic.test : OnOK1 : OnOK2 : OnOK3: no visible binding
  for global variable 'RAW.data'
snpXpert : logistic.test : OnOK1 : OnOK2 : OnOK3: no visible binding
  for global variable 'classID'
snpXpert : logistic.test : OnOK1 : OnOK2 : OnOK3: no visible binding
  for global variable 'Form.data'
snpXpert : logistic.test : OnOK1 : OnOK2 : OnOK3: no visible binding
  for global variable 'SNPlist.id.test'
snpXpert : logistic.test : OnOK1 : OnOK2 : OnOK3: no visible binding
  for global variable 'SNPMode'
snpXpert : logistic.test : OnOK1 : OnOK2 : OnOK3: no visible binding
  for global variable 'Cov.id'
snpXpert : logistic.test : OnOK1 : OnOK2 : OnOK3: no visible binding
  for '<<-' assignment to 'Log.result'
snpXpert : logistic.test : OnOK1 : OnOK2 : OnOK3: no visible binding
  for global variable 'Log.result'
snpXpert : LD.plot: no visible binding for '<<-' assignment to
  'list.name'
snpXpert : LD.plot: no visible binding for global variable 'RAW.data'
snpXpert : LD.plot: no visible binding for global variable 'list.name'
snpXpert : LD.plot : OnOK: no visible binding for global variable
  'list.name'
snpXpert : LD.plot : OnOK: no visible binding for '<<-' assignment to
  'SNPlist.id.test'
snpXpert : LD.plot : OnOK: no visible binding for global variable
  'SNPlist.id.test'
snpXpert : LD.plot : OnOK: no visible binding for global variable
  'Form.data'
snpXpert : add.plot.list: no visible binding for global variable 'tn'
snpXpert : haploScore: no visible binding for '<<-' assignment to
  'list.name'
snpXpert : haploScore: no visible binding for global variable
  'RAW.data'
snpXpert : haploScore: no visible binding for global variable
  'list.name'
snpXpert : haploScore : OnOK: no visible binding for global variable
  'list.name'
snpXpert : haploScore : OnOK: no visible binding for '<<-' assignment
  to 'SNPlist.id.test'
snpXpert : haploScore : OnOK: no visible binding for global variable
  'SNPlist.id.test'
snpXpert : haploScore : OnOK: no visible binding for global variable
  'Form.data'
snpXpert : haploScore : OnOK: no visible binding for global variable
  'RAW.data'
snpXpert : MDR: no visible binding for '<<-' assignment to 'list.name'
snpXpert : MDR: no visible binding for global variable 'RAW.data'
snpXpert : MDR: no visible binding for global variable 'list.name'
snpXpert : MDR : OnOK: no visible binding for global variable
  'list.name'
snpXpert : MDR : OnOK: no visible binding for '<<-' assignment to 'nbr'
snpXpert : MDR : OnOK: no visible binding for '<<-' assignment to
  'SNPlist.id.test'
snpXpert : MDR : OnOK: no visible binding for global variable
  'Form.data'
snpXpert : MDR : OnOK: no visible binding for global variable
  'SNPlist.id.test'
snpXpert : MDR : OnOK: no visible binding for global variable
  'RAW.data'
snpXpert : MDR : OnOK: no visible binding for global variable 'nbr'
* 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 examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'snpXpert-Ex.R' failed
The error most likely occurred in:

> ### Name: snpXpert
> ### Title: Software for analyzing SNP data
> ### Aliases: snpXpert
> ### Keywords: dplot utilities
> 
> ### ** Examples
> 
> snpXpert()
Warning in tclRequire("Iwidgets") : Tcl package 'Iwidgets' not found
Error in structure(.External("dotTclObjv", objv, PACKAGE = "tcltk"), class = "tclObj") : 
  [tcl] invalid command name "iwidgets::tabnotebook".
Calls: snpXpert ... .Tcl.args.objv -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'snpXpert-Ex.R' failed
The error most likely occurred in:

> ### Name: snpXpert
> ### Title: Software for analyzing SNP data
> ### Aliases: snpXpert
> ### Keywords: dplot utilities
> 
> ### ** Examples
> 
> snpXpert()
Warning in tclRequire("Iwidgets") : Tcl package 'Iwidgets' not found
Error in structure(.External("dotTclObjv", objv, PACKAGE = "tcltk"), class = "tclObj") : 
  [tcl] invalid command name "iwidgets::tabnotebook".
Calls: snpXpert ... .Tcl.args.objv -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted