* using log directory 'd:/Rcompile/CRANpkg/local/3.3/NSA.Rcheck' * using R version 3.3.2 (2016-10-31) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'NSA/DESCRIPTION' ... OK * this is package 'NSA' version '0.0.32' * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'R.methodsS3' 'MASS' 'matrixStats' 'R.oo' 'R.utils' 'aroma.core' 'aroma.affymetrix' 'DNAcopy' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 'NSA' can be installed ... OK * 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 * 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 use of S3 registration ... OK * checking dependencies in R code ... NOTE Packages in Depends field not imported from: 'DNAcopy' 'MASS' 'R.methodsS3' 'R.oo' 'aroma.affymetrix' 'aroma.core' 'matrixStats' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE NB: .First.lib is obsolete and will not be used in R >= 3.0.0 .First.lib: no visible global function definition for 'packageDescription' NSAByTotalAndFracB.matrix: no visible global function definition for 'throw' NSAByTotalAndFracB.matrix: no visible global function definition for 'str' NSANormalization: no visible global function definition for 'throw' NSANormalization: no visible global function definition for 'getChipType' NSANormalization: no visible global function definition for 'nbrOfFiles' NSANormalization: no visible global function definition for 'getNames' NSANormalization: no visible global function definition for 'extend' NSANormalization: no visible global function definition for 'Object' NSANormalization: no visible global function definition for 'setTags' SNPsNormalization: no visible global function definition for 'throw' SNPsNormalization: no visible global function definition for 'getChipType' SNPsNormalization: no visible global function definition for 'getNames' SNPsNormalization: no visible global function definition for 'extend' SNPsNormalization: no visible global function definition for 'Object' SNPsNormalization: no visible global function definition for 'setTags' SampleNormalization: no visible global function definition for 'throw' SampleNormalization: no visible global function definition for 'getChipType' SampleNormalization: no visible global function definition for 'nbrOfFiles' SampleNormalization: no visible global function definition for 'getNames' SampleNormalization: no visible global function definition for 'extend' SampleNormalization: no visible global function definition for 'Object' SampleNormalization: no visible global function definition for 'setTags' allocateOutputDataSets.NSANormalization: no visible global function definition for 'getPath' allocateOutputDataSets.NSANormalization: no visible global function definition for 'getName' allocateOutputDataSets.NSANormalization: no visible global function definition for 'getFile' allocateOutputDataSets.NSANormalization: no visible global function definition for 'getPathname' allocateOutputDataSets.NSANormalization: no visible global function definition for 'newInstance' allocateOutputDataSets.NSANormalization: no visible global function definition for 'throw' allocateOutputDataSets.NSANormalization: no visible global function definition for 'byPath' allocateOutputDataSets.SNPsNormalization: no visible global function definition for 'getPath' allocateOutputDataSets.SNPsNormalization: no visible global function definition for 'getName' allocateOutputDataSets.SNPsNormalization: no visible global function definition for 'getFile' allocateOutputDataSets.SNPsNormalization: no visible global function definition for 'nbrOfFiles' allocateOutputDataSets.SNPsNormalization: no visible global function definition for 'getPathname' allocateOutputDataSets.SNPsNormalization: no visible global function definition for 'newInstance' allocateOutputDataSets.SNPsNormalization: no visible global function definition for 'throw' allocateOutputDataSets.SNPsNormalization: no visible global function definition for 'byPath' allocateOutputDataSets.SNPsNormalization: no visible global function definition for 'getPathnames' allocateOutputDataSets.SampleNormalization: no visible global function definition for 'getPath' allocateOutputDataSets.SampleNormalization: no visible global function definition for 'getName' allocateOutputDataSets.SampleNormalization: no visible global function definition for 'getFile' allocateOutputDataSets.SampleNormalization: no visible global function definition for 'nbrOfFiles' allocateOutputDataSets.SampleNormalization: no visible global function definition for 'getPathname' allocateOutputDataSets.SampleNormalization: no visible global function definition for 'newInstance' allocateOutputDataSets.SampleNormalization: no visible global function definition for 'throw' allocateOutputDataSets.SampleNormalization: no visible global function definition for 'byPath' allocateOutputDataSets.SampleNormalization: no visible global function definition for 'getPathnames' findArraysTodo.NSANormalization: no visible global function definition for 'getNames' findArraysTodo.NSANormalization: no visible global function definition for 'getChipType' findArraysTodo.NSANormalization: no visible binding for global variable 'AffymetrixCdfFile' findArraysTodo.NSANormalization: no visible global function definition for 'getGenomeInformation' findArraysTodo.NSANormalization: no visible global function definition for 'getUnitsOnChromosome' findArraysTodo.NSANormalization: no visible global function definition for 'getFile' findArraysTodo.NSANormalization: no visible global function definition for 'getName' findArraysTodo.NSANormalization: no visible global function definition for 'str' findArraysTodo.SampleNormalization: no visible global function definition for 'getNames' findArraysTodo.SampleNormalization: no visible global function definition for 'getChipType' findArraysTodo.SampleNormalization: no visible binding for global variable 'AffymetrixCdfFile' findArraysTodo.SampleNormalization: no visible global function definition for 'getGenomeInformation' findArraysTodo.SampleNormalization: no visible global function definition for 'getUnitsOnChromosome' findArraysTodo.SampleNormalization: no visible global function definition for 'getFile' findArraysTodo.SampleNormalization: no visible global function definition for 'getName' findArraysTodo.SampleNormalization: no visible global function definition for 'str' findUnitsTodo.SNPsNormalization: no visible global function definition for 'getFullNames' findUnitsTodo.SNPsNormalization: no visible global function definition for 'str' findUnitsTodo.SNPsNormalization: no visible global function definition for 'getFile' fitNSA.matrix: no visible binding for global variable 'verbose' fitNSAcnPs.matrix: no visible global function definition for 'approxfun' fitOneNSA: no visible global function definition for 'hist' fitOneNSA: no visible global function definition for 'CNA' fitOneNSA: no visible global function definition for 'segment' fitSNPsN: no visible global function definition for 'rowMedians' fitSample: no visible global function definition for 'median' getFullName.NSANormalization: no visible global function definition for 'getName' getFullName.NSANormalization: no visible global function definition for 'getTags' getFullName.SNPsNormalization: no visible global function definition for 'getName' getFullName.SNPsNormalization: no visible global function definition for 'getTags' getFullName.SampleNormalization: no visible global function definition for 'getName' getFullName.SampleNormalization: no visible global function definition for 'getTags' getName.NSANormalization: no visible global function definition for 'getName' getName.SNPsNormalization: no visible global function definition for 'getName' getName.SampleNormalization: no visible global function definition for 'getName' getPath.NSANormalization: no visible global function definition for 'getRootPath' getPath.NSANormalization: no visible global function definition for 'getFullName' getPath.NSANormalization: no visible global function definition for 'getChipType' getPath.NSANormalization: no visible global function definition for 'getPath' getPath.NSANormalization: no visible global function definition for 'throw' getPath.SNPsNormalization: no visible global function definition for 'getRootPath' getPath.SNPsNormalization: no visible global function definition for 'getFullName' getPath.SNPsNormalization: no visible global function definition for 'getChipType' getPath.SNPsNormalization: no visible global function definition for 'getPath' getPath.SNPsNormalization: no visible global function definition for 'throw' getPath.SampleNormalization: no visible global function definition for 'getRootPath' getPath.SampleNormalization: no visible global function definition for 'getFullName' getPath.SampleNormalization: no visible global function definition for 'getChipType' getPath.SampleNormalization: no visible global function definition for 'getPath' getPath.SampleNormalization: no visible global function definition for 'throw' getTags.NSANormalization: no visible global function definition for 'getTags' getTags.NSANormalization: no visible global function definition for 'getAsteriskTags' getTags.SNPsNormalization: no visible global function definition for 'getTags' getTags.SNPsNormalization: no visible global function definition for 'getAsteriskTags' getTags.SampleNormalization: no visible global function definition for 'getTags' getTags.SampleNormalization: no visible global function definition for 'getAsteriskTags' nbrOfFiles.NSANormalization: no visible global function definition for 'nbrOfFiles' nbrOfFiles.SNPsNormalization: no visible global function definition for 'nbrOfFiles' nbrOfFiles.SampleNormalization: no visible global function definition for 'nbrOfFiles' process.NSANormalization: no visible global function definition for 'getChipType' process.NSANormalization: no visible binding for global variable 'AffymetrixCdfFile' process.NSANormalization: no visible global function definition for 'getGenomeInformation' process.NSANormalization: no visible global function definition for 'throw' process.NSANormalization: no visible global function definition for 'getRam' process.NSANormalization: no visible binding for global variable 'aromaSettings' process.NSANormalization: no visible global function definition for 'getNames' process.NSANormalization: no visible global function definition for 'getPath' process.NSANormalization: no visible global function definition for 'getFile' process.NSANormalization: no visible global function definition for 'getName' process.NSANormalization: no visible global function definition for 'getUnitsOnChromosome' process.NSANormalization: no visible global function definition for 'getPositions' process.NSANormalization: no visible global function definition for 'str' process.SNPsNormalization: no visible global function definition for 'throw' process.SNPsNormalization: no visible global function definition for 'getNames' process.SNPsNormalization: no visible global function definition for 'getFile' process.SNPsNormalization: no visible global function definition for 'findUnitsTodo' process.SNPsNormalization: no visible global function definition for 'getRam' process.SNPsNormalization: no visible binding for global variable 'aromaSettings' process.SNPsNormalization: no visible global function definition for 'str' process.SNPsNormalization: no visible global function definition for 'getChipType' process.SNPsNormalization: no visible global function definition for 'getPath' process.SNPsNormalization: no visible global function definition for 'extractMatrix' process.SNPsNormalization: no visible global function definition for 'getName' process.SNPsNormalization: no visible global function definition for 'getFullNames' process.SampleNormalization: no visible global function definition for 'getChipType' process.SampleNormalization: no visible binding for global variable 'AffymetrixCdfFile' process.SampleNormalization: no visible global function definition for 'getGenomeInformation' process.SampleNormalization: no visible global function definition for 'throw' process.SampleNormalization: no visible global function definition for 'getNames' process.SampleNormalization: no visible global function definition for 'getRam' process.SampleNormalization: no visible binding for global variable 'aromaSettings' process.SampleNormalization: no visible global function definition for 'getPath' process.SampleNormalization: no visible global function definition for 'getFile' process.SampleNormalization: no visible global function definition for 'getName' process.SampleNormalization: no visible global function definition for 'str' sampleNByTotalAndFracB.numeric: no visible global function definition for 'throw' sampleNByTotalAndFracB.numeric: no visible global function definition for 'str' setTags.NSANormalization: no visible global function definition for 'trim' setTags.SNPsNormalization: no visible global function definition for 'trim' setTags.SampleNormalization: no visible global function definition for 'trim' snpsNByTotalAndFracB.matrix: no visible global function definition for 'throw' snpsNByTotalAndFracB.matrix: no visible global function definition for 'str' snpsNByTotalAndFracB.matrix: no visible global function definition for 'rowAlls' Undefined global functions or variables: AffymetrixCdfFile CNA Object approxfun aromaSettings byPath extend extractMatrix findUnitsTodo getAsteriskTags getChipType getFile getFullName getFullNames getGenomeInformation getName getNames getPath getPathname getPathnames getPositions getRam getRootPath getTags getUnitsOnChromosome hist median nbrOfFiles newInstance packageDescription rowAlls rowMedians segment setTags str throw trim verbose Consider adding importFrom("graphics", "hist") importFrom("stats", "approxfun", "median") importFrom("utils", "packageDescription", "str") to your NAMESPACE file. * 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 ... [2s] OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs