• using R version 2.11.1 Patched (2010-07-29 r52657)
• 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 whether package 'snpXpert' can be installed ... 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
• 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 global function definition for 'HWE.chisq'
  snpXpert : HWE: no visible global function definition for 'genotype'
  snpXpert : HWE: no visible global function definition for 'HWE.exact'
  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: 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 : LD.plot : OnOK: no visible global function definition for
  'makeGenotypes'
  snpXpert : LD.plot : OnOK: no visible global function definition for
  'LD'
  snpXpert : add.plot.list: no visible binding for global variable 'tn'
  snpXpert : add.plot.list : <anonymous>: no visible global function
  definition for 'LDtable'
  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'
  Found possibly global 'T' or 'F' in the following function:
  snpXpert
• 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 examples ... ERROR
  Running examples in 'snpXpert-Ex.R' failed.
  The error most likely occurred in:
  
  > ### * snpXpert
  >
  > flush(stderr()); flush(stdout())
  >
  > ### 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 ... tkwidget -> tcl -> .Tcl.objv -> structure -> .External
  Execution halted