CRAN Package Check Results for Package MEET

Last updated on 2015-09-06 23:47:30.

Memtest notes: valgrind

Check Details

Version: 5.1.1
Check: package dependencies
Result: NOTE
    Depends: includes the non-default packages:
     ‘seqinr’ ‘pcaMethods’ ‘Matrix’ ‘ROCR’ ‘Hmisc’ ‘KernSmooth’ ‘seqLogo’
    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-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 5.1.1
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls to packages already attached by Depends:
     ‘Hmisc’ ‘KernSmooth’ ‘Matrix’ ‘ROCR’ ‘methods’ ‘pcaMethods’ ‘seqLogo’
     ‘seqinr’
     Please remove these calls from your code.
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-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 5.1.1
Check: R code for possible problems
Result: NOTE
    DivergenceDROSOPHILA: no visible global function definition for ‘data’
    DivergenceHOMO: no visible global function definition for ‘data’
    DivergenceMUS: no visible global function definition for ‘data’
    DivergenceRATTUS: no visible global function definition for ‘data’
    EntropyDROSOPHILA: no visible global function definition for ‘data’
    EntropyHOMO: no visible global function definition for ‘data’
    EntropyMUS: no visible global function definition for ‘data’
    EntropyRATTUS: no visible global function definition for ‘data’
    JacksonParameters: no visible global function definition for ‘prcomp’
    MEET: no visible global function definition for ‘write.table’
    MEET: no visible global function definition for ‘read.table’
    MEET: no visible global function definition for ‘data’
    PCanalysis: no visible global function definition for ‘residuals’
    PredictPCA: no visible global function definition for ‘residuals’
    QresidualsDROSOPHILA: no visible global function definition for ‘data’
    QresidualsHOMO: no visible global function definition for ‘data’
    QresidualsMUS: no visible global function definition for ‘data’
    QresidualsRATTUS: no visible global function definition for ‘data’
    QtoJackson: no visible global function definition for ‘pnorm’
    Read.aligned: no visible global function definition for ‘read.table’
    chooseModel : <anonymous>: no visible global function definition for
     ‘sd’
    pvalue: no visible global function definition for ‘sd’
    pvalue: no visible global function definition for ‘extendrange’
    writeMEME: no visible global function definition for ‘write.table’
    writeResultsHTML: no visible global function definition for ‘data’
    writeResultsHTML: no visible binding for global variable
     ‘RattusEntropy’
    writeResultsHTML: no visible binding for global variable
     ‘RattusDivergence’
    writeResultsHTML: no visible binding for global variable
     ‘RattusQresiduals’
    writeResultsHTML: no visible binding for global variable ‘MusEntropy’
    writeResultsHTML: no visible binding for global variable
     ‘MusDivergence’
    writeResultsHTML: no visible binding for global variable
     ‘MusQresiduals’
    writeResultsHTML: no visible binding for global variable
     ‘DrosophilaEntropy’
    writeResultsHTML: no visible binding for global variable
     ‘DrosophilaDivergence’
    writeResultsHTML: no visible binding for global variable
     ‘DrosophilaQresiduals’
    writeResultsHTML: no visible binding for global variable ‘HomoEntropy’
    writeResultsHTML: no visible binding for global variable
     ‘HomoDivergence’
    writeResultsHTML: no visible binding for global variable
     ‘HomoQresiduals’
    writeResultsHTML: no visible global function definition for ‘png’
    writeResultsHTML: no visible global function definition for ‘dev.off’
    Undefined global functions or variables:
     DrosophilaDivergence DrosophilaEntropy DrosophilaQresiduals
     HomoDivergence HomoEntropy HomoQresiduals MusDivergence MusEntropy
     MusQresiduals RattusDivergence RattusEntropy RattusQresiduals data
     dev.off extendrange png pnorm prcomp read.table residuals sd
     write.table
    Consider adding
     importFrom("grDevices", "dev.off", "extendrange", "png")
     importFrom("stats", "pnorm", "prcomp", "residuals", "sd")
     importFrom("utils", "data", "read.table", "write.table")
    to your NAMESPACE.
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-windows-ix86+x86_64

Version: 5.1.1
Check: Rd line widths
Result: NOTE
    Rd file 'MEET.Rd':
     \usage lines wider than 90 characters:
     MEET(TF,nameTF, seqin, alg, method, mode, org, vector, num_motif, len_motif, direction, threshold, order, model,position, mv, gapopen, ... [TRUNCATED]
    
    Rd file 'MIread.Rd':
     \examples lines wider than 100 characters:
     test<-MIread(training.set=iicc[["a1"]]$Transcriptionfactor, val.set=iicc[["a1"]]$Transcriptionfactor[1,],iicc=model)
    
    Rd file 'align.muscle.Rd':
     \usage lines wider than 90 characters:
     align.muscle(filein , fileout = "Sq.fa", gapopen = gapopen, maxiters = maxiters, gapextend = gapextend, call)
    
    These lines will be truncated in the PDF 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-patched-linux-x86_64, r-release-linux-x86_64