* using log directory 'd:/Rcompile/CRANpkg/local/2.8/snpXpert.Rcheck' * using R version 2.8.1 beta (2008-12-12 r47183) * 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 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 : : no visible binding for global variable 'Result.tt' snpXpert : : no visible binding for global variable 'SNPlist.id' snpXpert : : 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 : : 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 cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * creating snpXpert-Ex.R ... 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