CRAN Package Check Results for Package PMA

Last updated on 2015-08-28 21:46:52.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.9 6.61 45.16 51.78 NOTE
r-devel-linux-x86_64-debian-gcc 1.0.9 7.18 53.56 60.74 NOTE
r-devel-linux-x86_64-fedora-clang 1.0.9 106.79 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0.9 97.41 NOTE
r-devel-osx-x86_64-clang 1.0.9 86.11 NOTE
r-devel-windows-ix86+x86_64 1.0.9 39.00 160.00 199.00 NOTE
r-patched-linux-x86_64 1.0.9 7.68 56.64 64.32 NOTE
r-patched-solaris-sparc 1.0.9 795.50 NOTE
r-patched-solaris-x86 1.0.9 136.10 NOTE
r-release-linux-x86_64 1.0.9 7.31 57.77 65.08 NOTE
r-release-osx-x86_64-mavericks 1.0.9 NOTE
r-release-windows-ix86+x86_64 1.0.9 38.00 164.00 202.00 NOTE
r-oldrel-windows-ix86+x86_64 1.0.9 39.00 140.00 179.00 NOTE

Check Details

Version: 1.0.9
Check: installed package size
Result: NOTE
     installed size is 7.9Mb
     sub-directories of 1Mb or more:
     data 6.3Mb
     libs 1.3Mb
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: 1.0.9
Check: dependencies in R code
Result: NOTE
    Packages in Depends field not imported from:
     ‘impute’ ‘plyr’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
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: 1.0.9
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     plot.CCA.permute plot.MultiCCA.permute plot.PMDL1FL.cv
     plot.PMDL1L1.cv plot.SPC.cv print.CCA print.CCA.permute
     print.MultiCCA print.MultiCCA.permute print.PMDL1FL print.PMDL1FL.cv
     print.PMDL1L1 print.PMDL1L1.cv print.SPC print.SPC.cv
    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-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64

Version: 1.0.9
Check: R code for possible problems
Result: NOTE
    CCA: no visible binding for global variable ‘sd’
    CCA: no visible global function definition for ‘cor’
    CCA.permute.both: no visible global function definition for ‘cor’
    CCA.permute.both: no visible binding for global variable ‘sd’
    CCA.permute.justone: no visible global function definition for ‘cor’
    CCA.permute.justone: no visible global function definition for ‘sd’
    CCA.permute.xonly: no visible global function definition for ‘cor’
    CCA.permute.xonly: no visible binding for global variable ‘sd’
    CCA.permute.zonly: no visible global function definition for ‘cor’
    CCA.permute.zonly: no visible binding for global variable ‘sd’
    CCAPhenotypeZeroSome: no visible global function definition for
     ‘quantile’
    CCAPhenotypeZeroSome: no visible global function definition for ‘par’
    CGH.SMD: no visible global function definition for ‘rnorm’
    ChooseLambda1Lambda2: no visible global function definition for
     ‘lowess’
    ChooseLambda1Lambda2: no visible global function definition for
     ‘quantile’
    ChooseLambda1Lambda2old: no visible global function definition for
     ‘lowess’
    ChooseLambda1Lambda2old: no visible global function definition for
     ‘quantile’
    GetCors: no visible global function definition for ‘cor’
    MultiCCA.permute: no visible global function definition for ‘sd’
    PMDL1FL.cv: no visible global function definition for ‘runif’
    PMDL1FL.cv: no visible binding for global variable ‘sd’
    PMDL1L1.cv: no visible global function definition for ‘runif’
    PMDL1L1.cv: no visible binding for global variable ‘sd’
    SMD: no visible global function definition for ‘rnorm’
    SMDOrth: no visible global function definition for ‘rnorm’
    SMDOrth: no visible global function definition for ‘lsfit’
    SPC.cv: no visible global function definition for ‘runif’
    SPC.cv: no visible binding for global variable ‘sd’
    SparseCCA: no visible global function definition for ‘rnorm’
    cor.xl.ImputeData: no visible global function definition for
     ‘impute.knn’
    cor.xl.Plot1: no visible global function definition for ‘png’
    cor.xl.Plot1: no visible global function definition for ‘plot’
    cor.xl.Plot1: no visible global function definition for ‘dev.off’
    cor.xl.Plot2: no visible global function definition for ‘png’
    cor.xl.Plot2: no visible global function definition for ‘title’
    cor.xl.Plot2: no visible global function definition for ‘dev.off’
    cor.xl.Plot2a: no visible global function definition for ‘png’
    cor.xl.Plot2a: no visible global function definition for ‘title’
    cor.xl.Plot2a: no visible global function definition for ‘dev.off’
    cor.xl.Plot2b: no visible global function definition for ‘png’
    cor.xl.Plot2b: no visible global function definition for ‘title’
    cor.xl.Plot2b: no visible global function definition for ‘dev.off’
    cor.xl.Plot3: no visible global function definition for ‘png’
    cor.xl.Plot3: no visible global function definition for ‘title’
    cor.xl.Plot3: no visible global function definition for ‘dev.off’
    cor.xl.Plot3a: no visible global function definition for ‘png’
    cor.xl.Plot3a: no visible global function definition for ‘title’
    cor.xl.Plot3a: no visible global function definition for ‘dev.off’
    cor.xl.Plot3b: no visible global function definition for ‘png’
    cor.xl.Plot3b: no visible global function definition for ‘title’
    cor.xl.Plot3b: no visible global function definition for ‘dev.off’
    plot.CCA.permute: no visible global function definition for ‘par’
    plot.CCA.permute: no visible global function definition for ‘plot’
    plot.CCA.permute: no visible global function definition for ‘points’
    plot.CCA.permute: no visible global function definition for ‘lines’
    plot.CGH.FL.Single: no visible global function definition for ‘plot’
    plot.CGH.FL.Single: no visible global function definition for
     ‘segments’
    plot.CGH.FL.Single: no visible global function definition for ‘text’
    plot.MultiCCA.permute: no visible global function definition for ‘par’
    plot.MultiCCA.permute: no visible global function definition for ‘plot’
    plot.MultiCCA.permute: no visible global function definition for
     ‘points’
    plot.MultiCCA.permute: no visible global function definition for
     ‘lines’
    plot.PMDL1FL.cv: no visible global function definition for ‘par’
    plot.PMDL1FL.cv: no visible global function definition for ‘plot’
    plot.PMDL1FL.cv: no visible global function definition for ‘points’
    plot.PMDL1FL.cv: no visible global function definition for ‘lines’
    plot.PMDL1L1.cv: no visible global function definition for ‘plot’
    plot.PMDL1L1.cv: no visible global function definition for ‘points’
    plot.PMDL1L1.cv: no visible global function definition for ‘lines’
    plot.SPC.cv: no visible global function definition for ‘plot’
    plot.SPC.cv: no visible global function definition for ‘points’
    plot.SPC.cv: no visible global function definition for ‘lines’
    safesvd: no visible global function definition for ‘rnorm’
    Undefined global functions or variables:
     cor dev.off impute.knn lines lowess lsfit par plot png points
     quantile rnorm runif sd segments text title
    Consider adding
     importFrom("grDevices", "dev.off", "png")
     importFrom("graphics", "lines", "par", "plot", "points", "segments",
     "text", "title")
     importFrom("stats", "cor", "lowess", "lsfit", "quantile", "rnorm",
     "runif", "sd")
    to your NAMESPACE.
    
    Found the following assignments to the global environment:
    File ‘PMA/R/CCA.xlfuns.R’:
     assign(paste("cor.", x, sep = ""), val, pos = .GlobalEnv)
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang

Version: 1.0.9
Check: Rd line widths
Result: NOTE
    Rd file 'CCA.Rd':
     \usage lines wider than 90 characters:
     CCA(x, z, typex=c("standard", "ordered"),typez=c("standard","ordered"), penaltyx=NULL, penaltyz=NULL, K=1,
     \examples lines wider than 100 characters:
     out <- CCA(x,z,typex="standard",typez="standard",K=1,penaltyx=perm.out$bestpenaltyx,penaltyz=perm.out$bestpenaltyz, v=perm.out$v.init)
     #out <- CCA(x,z,typex="standard",typez="standard",K=1,penaltyx=perm.out$bestpenaltyx,penaltyz=perm.out$bestpenaltyz,
     #out<-CCA(x,z,typex="standard",typez="standard",outcome="quantitative",y=y,penaltyx=perm.out$bestpenaltyx,penaltyz=perm.out$bestpenalty ... [TRUNCATED]
     #perm.out <- CCA.permute(x=rna,z=dna[,chrom==1],typex="standard", typez="ordered",nperms=5,penaltyxs=seq(.02,.7,len=10))
     #out <- CCA(x=rna,z=dna[,chrom==1], typex="standard", typez="ordered",penaltyx=perm.out$bestpenaltyx,
    
    Rd file 'CCA.permute.Rd':
     \usage lines wider than 90 characters:
     CCA.permute(x,z,typex=c("standard", "ordered"),typez=c("standard","ordered"), penaltyxs=NULL, penaltyzs=NULL,
    
    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

Version: 1.0.9
Check: R code for possible problems
Result: NOTE
    CCA: no visible binding for global variable ‘sd’
    CCA: no visible global function definition for ‘cor’
    CCA.permute.both: no visible global function definition for ‘cor’
    CCA.permute.both: no visible binding for global variable ‘sd’
    CCA.permute.justone: no visible global function definition for ‘cor’
    CCA.permute.justone: no visible global function definition for ‘sd’
    CCA.permute.xonly: no visible global function definition for ‘cor’
    CCA.permute.xonly: no visible binding for global variable ‘sd’
    CCA.permute.zonly: no visible global function definition for ‘cor’
    CCA.permute.zonly: no visible binding for global variable ‘sd’
    CCAPhenotypeZeroSome: no visible global function definition for
     ‘quantile’
    CCAPhenotypeZeroSome: no visible global function definition for ‘par’
    CGH.SMD: no visible global function definition for ‘rnorm’
    ChooseLambda1Lambda2: no visible global function definition for
     ‘lowess’
    ChooseLambda1Lambda2: no visible global function definition for
     ‘quantile’
    ChooseLambda1Lambda2old: no visible global function definition for
     ‘lowess’
    ChooseLambda1Lambda2old: no visible global function definition for
     ‘quantile’
    GetCors: no visible global function definition for ‘cor’
    MultiCCA.permute: no visible global function definition for ‘sd’
    PMDL1FL.cv: no visible global function definition for ‘runif’
    PMDL1FL.cv: no visible binding for global variable ‘sd’
    PMDL1L1.cv: no visible global function definition for ‘runif’
    PMDL1L1.cv: no visible binding for global variable ‘sd’
    SMD: no visible global function definition for ‘rnorm’
    SMDOrth: no visible global function definition for ‘rnorm’
    SMDOrth: no visible global function definition for ‘lsfit’
    SPC.cv: no visible global function definition for ‘runif’
    SPC.cv: no visible binding for global variable ‘sd’
    SparseCCA: no visible global function definition for ‘rnorm’
    cor.xl.ImputeData: no visible global function definition for
     ‘impute.knn’
    cor.xl.Plot1: no visible global function definition for ‘png’
    cor.xl.Plot1: no visible global function definition for ‘plot’
    cor.xl.Plot1: no visible global function definition for ‘dev.off’
    cor.xl.Plot2: no visible global function definition for ‘png’
    cor.xl.Plot2: no visible global function definition for ‘title’
    cor.xl.Plot2: no visible global function definition for ‘dev.off’
    cor.xl.Plot2a: no visible global function definition for ‘png’
    cor.xl.Plot2a: no visible global function definition for ‘title’
    cor.xl.Plot2a: no visible global function definition for ‘dev.off’
    cor.xl.Plot2b: no visible global function definition for ‘png’
    cor.xl.Plot2b: no visible global function definition for ‘title’
    cor.xl.Plot2b: no visible global function definition for ‘dev.off’
    cor.xl.Plot3: no visible global function definition for ‘png’
    cor.xl.Plot3: no visible global function definition for ‘title’
    cor.xl.Plot3: no visible global function definition for ‘dev.off’
    cor.xl.Plot3a: no visible global function definition for ‘png’
    cor.xl.Plot3a: no visible global function definition for ‘title’
    cor.xl.Plot3a: no visible global function definition for ‘dev.off’
    cor.xl.Plot3b: no visible global function definition for ‘png’
    cor.xl.Plot3b: no visible global function definition for ‘title’
    cor.xl.Plot3b: no visible global function definition for ‘dev.off’
    plot.CCA.permute: no visible global function definition for ‘par’
    plot.CCA.permute: no visible global function definition for ‘plot’
    plot.CCA.permute: no visible global function definition for ‘points’
    plot.CCA.permute: no visible global function definition for ‘lines’
    plot.CGH.FL.Single: no visible global function definition for ‘plot’
    plot.CGH.FL.Single: no visible global function definition for
     ‘segments’
    plot.CGH.FL.Single: no visible global function definition for ‘text’
    plot.MultiCCA.permute: no visible global function definition for ‘par’
    plot.MultiCCA.permute: no visible global function definition for ‘plot’
    plot.MultiCCA.permute: no visible global function definition for
     ‘points’
    plot.MultiCCA.permute: no visible global function definition for
     ‘lines’
    plot.PMDL1FL.cv: no visible global function definition for ‘par’
    plot.PMDL1FL.cv: no visible global function definition for ‘plot’
    plot.PMDL1FL.cv: no visible global function definition for ‘points’
    plot.PMDL1FL.cv: no visible global function definition for ‘lines’
    plot.PMDL1L1.cv: no visible global function definition for ‘plot’
    plot.PMDL1L1.cv: no visible global function definition for ‘points’
    plot.PMDL1L1.cv: no visible global function definition for ‘lines’
    plot.SPC.cv: no visible global function definition for ‘plot’
    plot.SPC.cv: no visible global function definition for ‘points’
    plot.SPC.cv: no visible global function definition for ‘lines’
    safesvd: no visible global function definition for ‘rnorm’
    Undefined global functions or variables:
     cor dev.off impute.knn lines lowess lsfit par plot png points
     quantile rnorm runif sd segments text title
    Consider adding
     importFrom("grDevices", "dev.off", "png")
     importFrom("graphics", "lines", "par", "plot", "points", "segments",
     "text", "title")
     importFrom("stats", "cor", "lowess", "lsfit", "quantile", "rnorm",
     "runif", "sd")
    to your NAMESPACE.
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.0.9
Check: R code for possible problems
Result: NOTE
    cor.xl.ImputeData: no visible global function definition for
     ‘impute.knn’
    Undefined global functions or variables:
     impute.knn
    
    Found the following assignments to the global environment:
    File ‘PMA/R/CCA.xlfuns.R’:
     assign(paste("cor.", x, sep = ""), val, pos = .GlobalEnv)
Flavor: r-devel-osx-x86_64-clang

Version: 1.0.9
Check: R code for possible problems
Result: NOTE
    CCA: no visible binding for global variable 'sd'
    CCA: no visible global function definition for 'cor'
    CCA.permute.both: no visible global function definition for
     'winProgressBar'
    CCA.permute.both: no visible global function definition for
     'setWinProgressBar'
    CCA.permute.both: no visible global function definition for 'cor'
    CCA.permute.both: no visible binding for global variable 'sd'
    CCA.permute.justone: no visible global function definition for
     'winProgressBar'
    CCA.permute.justone: no visible global function definition for
     'setWinProgressBar'
    CCA.permute.justone: no visible global function definition for 'cor'
    CCA.permute.justone: no visible global function definition for 'sd'
    CCA.permute.xonly: no visible global function definition for
     'winProgressBar'
    CCA.permute.xonly: no visible global function definition for
     'setWinProgressBar'
    CCA.permute.xonly: no visible global function definition for 'cor'
    CCA.permute.xonly: no visible binding for global variable 'sd'
    CCA.permute.zonly: no visible global function definition for
     'winProgressBar'
    CCA.permute.zonly: no visible global function definition for
     'setWinProgressBar'
    CCA.permute.zonly: no visible global function definition for 'cor'
    CCA.permute.zonly: no visible binding for global variable 'sd'
    CCAPhenotypeZeroSome: no visible global function definition for
     'quantile'
    CCAPhenotypeZeroSome: no visible global function definition for 'par'
    CGH.SMD: no visible global function definition for 'rnorm'
    ChooseLambda1Lambda2: no visible global function definition for
     'lowess'
    ChooseLambda1Lambda2: no visible global function definition for
     'quantile'
    ChooseLambda1Lambda2old: no visible global function definition for
     'lowess'
    ChooseLambda1Lambda2old: no visible global function definition for
     'quantile'
    GetCors: no visible global function definition for 'cor'
    MultiCCA.permute: no visible global function definition for 'sd'
    PMDL1FL.cv: no visible global function definition for 'runif'
    PMDL1FL.cv: no visible binding for global variable 'sd'
    PMDL1L1.cv: no visible global function definition for 'runif'
    PMDL1L1.cv: no visible binding for global variable 'sd'
    SMD: no visible global function definition for 'rnorm'
    SMDOrth: no visible global function definition for 'rnorm'
    SMDOrth: no visible global function definition for 'lsfit'
    SPC.cv: no visible global function definition for 'runif'
    SPC.cv: no visible binding for global variable 'sd'
    SparseCCA: no visible global function definition for 'rnorm'
    cor.xl.ImputeData: no visible global function definition for
     'impute.knn'
    cor.xl.Plot1: no visible global function definition for 'png'
    cor.xl.Plot1: no visible global function definition for 'plot'
    cor.xl.Plot1: no visible global function definition for 'dev.off'
    cor.xl.Plot2: no visible global function definition for 'png'
    cor.xl.Plot2: no visible global function definition for 'title'
    cor.xl.Plot2: no visible global function definition for 'dev.off'
    cor.xl.Plot2a: no visible global function definition for 'png'
    cor.xl.Plot2a: no visible global function definition for 'title'
    cor.xl.Plot2a: no visible global function definition for 'dev.off'
    cor.xl.Plot2b: no visible global function definition for 'png'
    cor.xl.Plot2b: no visible global function definition for 'title'
    cor.xl.Plot2b: no visible global function definition for 'dev.off'
    cor.xl.Plot3: no visible global function definition for 'png'
    cor.xl.Plot3: no visible global function definition for 'title'
    cor.xl.Plot3: no visible global function definition for 'dev.off'
    cor.xl.Plot3a: no visible global function definition for 'png'
    cor.xl.Plot3a: no visible global function definition for 'title'
    cor.xl.Plot3a: no visible global function definition for 'dev.off'
    cor.xl.Plot3b: no visible global function definition for 'png'
    cor.xl.Plot3b: no visible global function definition for 'title'
    cor.xl.Plot3b: no visible global function definition for 'dev.off'
    cor.xl.error.trace: no visible global function definition for
     'winDialog'
    plot.CCA.permute: no visible global function definition for 'par'
    plot.CCA.permute: no visible global function definition for 'plot'
    plot.CCA.permute: no visible global function definition for 'points'
    plot.CCA.permute: no visible global function definition for 'lines'
    plot.CGH.FL.Single: no visible global function definition for 'plot'
    plot.CGH.FL.Single: no visible global function definition for
     'segments'
    plot.CGH.FL.Single: no visible global function definition for 'text'
    plot.MultiCCA.permute: no visible global function definition for 'par'
    plot.MultiCCA.permute: no visible global function definition for 'plot'
    plot.MultiCCA.permute: no visible global function definition for
     'points'
    plot.MultiCCA.permute: no visible global function definition for
     'lines'
    plot.PMDL1FL.cv: no visible global function definition for 'par'
    plot.PMDL1FL.cv: no visible global function definition for 'plot'
    plot.PMDL1FL.cv: no visible global function definition for 'points'
    plot.PMDL1FL.cv: no visible global function definition for 'lines'
    plot.PMDL1L1.cv: no visible global function definition for 'plot'
    plot.PMDL1L1.cv: no visible global function definition for 'points'
    plot.PMDL1L1.cv: no visible global function definition for 'lines'
    plot.SPC.cv: no visible global function definition for 'plot'
    plot.SPC.cv: no visible global function definition for 'points'
    plot.SPC.cv: no visible global function definition for 'lines'
    safesvd: no visible global function definition for 'rnorm'
    Undefined global functions or variables:
     cor dev.off impute.knn lines lowess lsfit par plot png points
     quantile rnorm runif sd segments setWinProgressBar text title
     winDialog winProgressBar
    Consider adding
     importFrom("grDevices", "dev.off", "png")
     importFrom("graphics", "lines", "par", "plot", "points", "segments",
     "text", "title")
     importFrom("stats", "cor", "lowess", "lsfit", "quantile", "rnorm",
     "runif", "sd")
     importFrom("utils", "setWinProgressBar", "winDialog", "winProgressBar")
    to your NAMESPACE.
Flavor: r-devel-windows-ix86+x86_64

Version: 1.0.9
Check: R code for possible problems
Result: NOTE
    cor.xl.ImputeData: no visible global function definition for
     ‘impute.knn’
    
    Found the following assignments to the global environment:
    File ‘PMA/R/CCA.xlfuns.R’:
     assign(paste("cor.", x, sep = ""), val, pos = .GlobalEnv)
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.0.9
Check: R code for possible problems
Result: NOTE
    cor.xl.ImputeData: no visible global function definition for
     ‘impute.knn’
Flavors: r-patched-solaris-sparc, r-patched-solaris-x86, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64