CRAN Package Check Results for Package MEET

Last updated on 2017-04-29 23:50:32.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 5.1.1 7.70 76.87 84.57 NOTE
r-devel-linux-x86_64-debian-gcc 5.1.1 7.13 77.80 84.93 NOTE
r-devel-linux-x86_64-fedora-clang 5.1.1 170.41 NOTE --no-stop-on-test-error
r-devel-linux-x86_64-fedora-gcc 5.1.1 174.38 NOTE --no-stop-on-test-error
r-devel-windows-ix86+x86_64 5.1.1 59.00 244.00 303.00 NOTE
r-patched-linux-x86_64 5.1.1 6.63 74.59 81.22 NOTE
r-patched-solaris-sparc 5.1.1 1001.00 NOTE
r-patched-solaris-x86 5.1.1 213.50 NOTE
r-release-linux-x86_64 5.1.1 6.95 73.06 80.01 NOTE
r-release-windows-ix86+x86_64 5.1.1 48.00 223.00 271.00 NOTE
r-release-osx-x86_64 5.1.1 ERROR
r-oldrel-windows-ix86+x86_64 5.1.1 62.00 235.00 297.00 NOTE
r-oldrel-osx-x86_64 5.1.1 NOTE

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-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-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-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-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 file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, 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-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-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-patched-linux-x86_64, r-release-linux-x86_64

Version: 5.1.1
Check: compiled code
Result: NOTE
    File ‘MEET/libs/MEET.so’:
     Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
    
    It is good practice to register native routines and to disable symbol
    search.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 5.1.1
Flags: --no-stop-on-test-error
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-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 5.1.1
Flags: --no-stop-on-test-error
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-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 5.1.1
Flags: --no-stop-on-test-error
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 file.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 5.1.1
Flags: --no-stop-on-test-error
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-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 5.1.1
Flags: --no-stop-on-test-error
Check: compiled code
Result: NOTE
    File ‘MEET/libs/MEET.so’:
     Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
    
    It is good practice to register native routines and to disable symbol
    search.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 5.1.1
Check: package dependencies
Result: ERROR
    Packages required but not available: ‘pcaMethods’ ‘seqLogo’
    
    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.
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-osx-x86_64