CRAN Package Check Results for Package cghFLasso

Last updated on 2017-05-25 06:47:37.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.2-1 1.41 16.28 17.69 NOTE
r-devel-linux-x86_64-debian-gcc 0.2-1 1.26 16.53 17.79 NOTE
r-devel-linux-x86_64-fedora-clang 0.2-1 31.60 NOTE --no-stop-on-test-error
r-devel-linux-x86_64-fedora-gcc 0.2-1 29.50 NOTE --no-stop-on-test-error
r-devel-windows-ix86+x86_64 0.2-1 14.00 58.00 72.00 NOTE
r-patched-linux-x86_64 0.2-1 1.39 16.35 17.74 NOTE
r-patched-solaris-sparc 0.2-1 193.90 NOTE
r-patched-solaris-x86 0.2-1 41.70 NOTE
r-release-linux-x86_64 0.2-1 1.27 15.99 17.26 NOTE
r-release-windows-ix86+x86_64 0.2-1 7.00 44.00 51.00 NOTE
r-release-osx-x86_64 0.2-1 NOTE
r-oldrel-windows-ix86+x86_64 0.2-1 6.00 39.00 45.00 NOTE
r-oldrel-osx-x86_64 0.2-1 NOTE

Additional issues

rchk

Check Details

Version: 0.2-1
Check: DESCRIPTION meta-information
Result: NOTE
    Malformed Title field: should not end in a period.
    Malformed Description field: should contain one or more complete sentences.
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-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.2-1
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     plot.cghFLasso print.summary.cghFLasso summary.cghFLasso
    See section ‘Registering S3 methods’ 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-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64

Version: 0.2-1
Check: R code for possible problems
Result: NOTE
    CGH.fused.lasso.one.fast: no visible global function definition for
     ‘lowess’
    L2L1ExpandFit: no visible global function definition for
     ‘L2L1PathExtract’
    consensusFDR: no visible global function definition for ‘pbinom’
    my.mad: no visible global function definition for ‘median’
    output.cghFLasso: no visible global function definition for
     ‘write.table’
    plot.CGH.FL.All: no visible global function definition for ‘plot’
    plot.CGH.FL.All: no visible global function definition for ‘segments’
    plot.CGH.FL.All: no visible global function definition for ‘text’
    plot.CGH.FL.Consensus: no visible global function definition for
     ‘rainbow’
    plot.CGH.FL.Consensus: no visible global function definition for ‘plot’
    plot.CGH.FL.Consensus: no visible global function definition for
     ‘segments’
    plot.CGH.FL.Consensus: no visible global function definition for ‘gray’
    plot.CGH.FL.Consensus: no visible global function definition for ‘text’
    plot.CGH.FL.Single: no visible global function definition for ‘plot’
    plot.CGH.FL.Single: no visible global function definition for ‘gray’
    plot.CGH.FL.Single: no visible global function definition for
     ‘segments’
    plot.CGH.FL.Single: no visible global function definition for ‘text’
    plot.cghFLasso: no visible global function definition for ‘plot’
    plot.cghFLasso: no visible global function definition for ‘gray’
    plot.cghFLasso: no visible global function definition for ‘abline’
    plot.cghFLasso: no visible global function definition for ‘points’
    segment.score: no visible global function definition for ‘pnorm’
    Undefined global functions or variables:
     L2L1PathExtract abline gray lowess median pbinom plot pnorm points
     rainbow segments text write.table
    Consider adding
     importFrom("grDevices", "gray", "rainbow")
     importFrom("graphics", "abline", "plot", "points", "segments", "text")
     importFrom("stats", "lowess", "median", "pbinom", "pnorm")
     importFrom("utils", "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-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.2-1
Check: Rd line widths
Result: NOTE
    Rd file 'cghFLasso.Rd':
     \usage lines wider than 90 characters:
     cghFLasso(CGH.Array, chromosome=NULL, nucleotide.position=NULL, FL.norm=NULL, FDR=NULL, filter=NULL, missing.PlugIn=TRUE, smooth.size=5 ... [TRUNCATED]
     \examples lines wider than 100 characters:
     Disease.FL<-cghFLasso(CGH$DiseaseArray, chromosome=CGH$chromosome, nucleotide.position=CGH$nucposition, FL.norm=Normal.FL, FDR=0.01)
    
    Rd file 'cghFLasso.ref.Rd':
     \examples lines wider than 100 characters:
     Disease.FL<-cghFLasso(CGH$DiseaseArray, chromosome=CGH$chromosome, nucleotide.position=CGH$nucposition, FL.norm=Normal.FL, FDR=0.01)
    
    Rd file 'output.cghFLasso.Rd':
     \examples lines wider than 100 characters:
     Disease.FL<-cghFLasso(CGH$DiseaseArray, chromosome=CGH$chromosome, nucleotide.position=CGH$nucposition, FL.norm=Normal.FL, FDR=0.01)
    
    Rd file 'plot.cghFLasso.Rd':
     \examples lines wider than 100 characters:
     Disease.FL<-cghFLasso(CGH$DiseaseArray, chromosome=CGH$chromosome, nucleotide.position=CGH$nucposition, FL.norm=Normal.FL, FDR=0.01)
    
    Rd file 'summary.cghFLasso.Rd':
     \examples lines wider than 100 characters:
     Disease.FL<-cghFLasso(CGH$DiseaseArray, chromosome=CGH$chromosome, nucleotide.position=CGH$nucposition, FL.norm=Normal.FL, FDR=0.01)
    
    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: 0.2-1
Check: Rd \usage sections
Result: NOTE
    S3 methods shown with full name in documentation object 'plot.cghFLasso':
     ‘plot.cghFLasso’
    
    S3 methods shown with full name in documentation object 'summary.cghFLasso':
     ‘summary.cghFLasso’ ‘print.summary.cghFLasso’
    
    The \usage entries for S3 methods should use the \method markup and not
    their full name.
    See chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ manual.
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-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.2-1
Check: compiled code
Result: NOTE
    File ‘cghFLasso/libs/cghFLasso.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: 0.2-1
Flags: --no-stop-on-test-error
Check: DESCRIPTION meta-information
Result: NOTE
    Malformed Title field: should not end in a period.
    Malformed Description field: should contain one or more complete sentences.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.2-1
Flags: --no-stop-on-test-error
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     plot.cghFLasso print.summary.cghFLasso summary.cghFLasso
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.2-1
Flags: --no-stop-on-test-error
Check: R code for possible problems
Result: NOTE
    CGH.fused.lasso.one.fast: no visible global function definition for
     ‘lowess’
    L2L1ExpandFit: no visible global function definition for
     ‘L2L1PathExtract’
    consensusFDR: no visible global function definition for ‘pbinom’
    my.mad: no visible global function definition for ‘median’
    output.cghFLasso: no visible global function definition for
     ‘write.table’
    plot.CGH.FL.All: no visible global function definition for ‘plot’
    plot.CGH.FL.All: no visible global function definition for ‘segments’
    plot.CGH.FL.All: no visible global function definition for ‘text’
    plot.CGH.FL.Consensus: no visible global function definition for
     ‘rainbow’
    plot.CGH.FL.Consensus: no visible global function definition for ‘plot’
    plot.CGH.FL.Consensus: no visible global function definition for
     ‘segments’
    plot.CGH.FL.Consensus: no visible global function definition for ‘gray’
    plot.CGH.FL.Consensus: no visible global function definition for ‘text’
    plot.CGH.FL.Single: no visible global function definition for ‘plot’
    plot.CGH.FL.Single: no visible global function definition for ‘gray’
    plot.CGH.FL.Single: no visible global function definition for
     ‘segments’
    plot.CGH.FL.Single: no visible global function definition for ‘text’
    plot.cghFLasso: no visible global function definition for ‘plot’
    plot.cghFLasso: no visible global function definition for ‘gray’
    plot.cghFLasso: no visible global function definition for ‘abline’
    plot.cghFLasso: no visible global function definition for ‘points’
    segment.score: no visible global function definition for ‘pnorm’
    Undefined global functions or variables:
     L2L1PathExtract abline gray lowess median pbinom plot pnorm points
     rainbow segments text write.table
    Consider adding
     importFrom("grDevices", "gray", "rainbow")
     importFrom("graphics", "abline", "plot", "points", "segments", "text")
     importFrom("stats", "lowess", "median", "pbinom", "pnorm")
     importFrom("utils", "write.table")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.2-1
Flags: --no-stop-on-test-error
Check: Rd line widths
Result: NOTE
    Rd file 'cghFLasso.Rd':
     \usage lines wider than 90 characters:
     cghFLasso(CGH.Array, chromosome=NULL, nucleotide.position=NULL, FL.norm=NULL, FDR=NULL, filter=NULL, missing.PlugIn=TRUE, smooth.size=5 ... [TRUNCATED]
     \examples lines wider than 100 characters:
     Disease.FL<-cghFLasso(CGH$DiseaseArray, chromosome=CGH$chromosome, nucleotide.position=CGH$nucposition, FL.norm=Normal.FL, FDR=0.01)
    
    Rd file 'cghFLasso.ref.Rd':
     \examples lines wider than 100 characters:
     Disease.FL<-cghFLasso(CGH$DiseaseArray, chromosome=CGH$chromosome, nucleotide.position=CGH$nucposition, FL.norm=Normal.FL, FDR=0.01)
    
    Rd file 'output.cghFLasso.Rd':
     \examples lines wider than 100 characters:
     Disease.FL<-cghFLasso(CGH$DiseaseArray, chromosome=CGH$chromosome, nucleotide.position=CGH$nucposition, FL.norm=Normal.FL, FDR=0.01)
    
    Rd file 'plot.cghFLasso.Rd':
     \examples lines wider than 100 characters:
     Disease.FL<-cghFLasso(CGH$DiseaseArray, chromosome=CGH$chromosome, nucleotide.position=CGH$nucposition, FL.norm=Normal.FL, FDR=0.01)
    
    Rd file 'summary.cghFLasso.Rd':
     \examples lines wider than 100 characters:
     Disease.FL<-cghFLasso(CGH$DiseaseArray, chromosome=CGH$chromosome, nucleotide.position=CGH$nucposition, FL.norm=Normal.FL, FDR=0.01)
    
    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: 0.2-1
Flags: --no-stop-on-test-error
Check: Rd \usage sections
Result: NOTE
    S3 methods shown with full name in documentation object 'plot.cghFLasso':
     ‘plot.cghFLasso’
    
    S3 methods shown with full name in documentation object 'summary.cghFLasso':
     ‘summary.cghFLasso’ ‘print.summary.cghFLasso’
    
    The \usage entries for S3 methods should use the \method markup and not
    their full name.
    See chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.2-1
Flags: --no-stop-on-test-error
Check: compiled code
Result: NOTE
    File ‘cghFLasso/libs/cghFLasso.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