CRAN Package Check Results for Package NSA

Last updated on 2014-09-12 01:48:10.

Check Details

Version: 0.0.32
Check: package dependencies
Result: 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.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64

Version: 0.0.32
Check: dependencies in R code
Result: 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.
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.0.32
Check: R code for possible problems
Result: NOTE
    NB: .First.lib is obsolete and will not be used in R >= 3.0.0
    
    NSAByTotalAndFracB.matrix: no visible global function definition for
     ‘throw’
    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.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’
    findUnitsTodo.SNPsNormalization: no visible global function definition
     for ‘getFullNames’
    findUnitsTodo.SNPsNormalization: no visible global function definition
     for ‘getFile’
    fitNSA.matrix: no visible binding for global variable ‘verbose’
    fitOneNSA: no visible global function definition for ‘CNA’
    fitOneNSA: no visible global function definition for ‘segment’
    fitSNPsN: no visible global function definition for ‘rowMedians’
    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.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
     ‘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’
    sampleNByTotalAndFracB.numeric: no visible global function definition
     for ‘throw’
    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
     ‘rowAlls’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64

Version: 0.0.32
Check: top-level files
Result: NOTE
    Non-standard file/directory found at top level:
     ‘incl’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.0.32
Check: Rd line widths
Result: NOTE
    Rd file 'NSANormalization.Rd':
     \examples lines wider than 100 characters:
     by <- 50e3; # 50kb bins; you may want to try with other amounts of smoothing xOut <- seq(from=xRange[1], to=xRange[2], by=by);
     plot(getSignals(cnCNPS), getSignals(cnSNPS), xlim=Clim, ylim=Clim); abline(a=0, b=1, col="red", lwd=2);
    
    These lines will be truncated in the PDF manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.0.32
Check: R code for possible problems
Result: NOTE
    NB: .First.lib is obsolete and will not be used in R >= 3.0.0
Flavors: r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64