• using R Under development (unstable) (2012-05-22 r59405)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• 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 ... WARNING
  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 for executable files ... OK
• checking whether package ‘snpXpert’ can be installed ... OK
• checking installed package size ... OK
• checking package directory ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... 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 loading without being on the library search path ... 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 : 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: 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: 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 ... OK
• checking PDF version of manual ... OK
  WARNING: There was 1 warning.
  NOTE: There was 1 note.
  See
  ‘/data/gannet/tmp/ripley/R/packages/tests-devel/snpXpert.Rcheck/00check.log’
  for details.