CRAN Package Check Results for Package PMA

Last updated on 2015-07-02 21:46:57.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.9 6.30 47.54 53.84 NOTE
r-devel-linux-x86_64-debian-gcc 1.0.9 7.14 46.65 53.79 NOTE
r-devel-linux-x86_64-fedora-clang 1.0.9 110.27 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0.9 103.32 NOTE
r-devel-osx-x86_64-clang 1.0.9 91.91 NOTE
r-devel-windows-ix86+x86_64 1.0.9 27.00 109.00 136.00 NOTE
r-patched-linux-x86_64 1.0.9 7.23 47.66 54.88 NOTE
r-patched-solaris-sparc 1.0.9 795.30 NOTE
r-patched-solaris-x86 1.0.9 131.70 NOTE
r-release-linux-x86_64 1.0.9 7.31 47.54 54.85 NOTE
r-release-osx-x86_64-mavericks 1.0.9 NOTE
r-release-windows-ix86+x86_64 1.0.9 28.00 117.00 145.00 NOTE
r-oldrel-windows-ix86+x86_64 1.0.9 31.00 121.00 152.00 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
    
    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-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’
    
    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-linux-x86_64-debian-gcc

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
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'
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