CRAN Package Check Results for Package PMA

Last updated on 2015-03-30 17:49:10.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.9 6.39 48.06 54.45 NOTE
r-devel-linux-x86_64-debian-gcc 1.0.9 7.53 48.72 56.25 NOTE
r-devel-linux-x86_64-fedora-clang 1.0.9 111.44 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0.9 103.14 NOTE
r-devel-osx-x86_64-clang 1.0.9 94.88 NOTE
r-prerel-windows-ix86+x86_64 1.0.9 31.00 112.00 143.00 NOTE
r-prerel-linux-x86_64 1.0.9 7.23 47.05 54.28 NOTE
r-prerel-solaris-sparc 1.0.9 794.60 NOTE
r-prerel-solaris-x86 1.0.9 132.50 NOTE
r-release-linux-x86_64 1.0.9 7.60 53.66 61.27 NOTE
r-release-osx-x86_64-mavericks 1.0.9 NOTE
r-release-osx-x86_64-snowleopard 1.0.9 NOTE
r-release-windows-ix86+x86_64 1.0.9 30.00 120.00 150.00 NOTE
r-oldrel-windows-ix86+x86_64 1.0.9 31.00 123.00 154.00 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-prerel-windows-ix86+x86_64, r-prerel-linux-x86_64, r-prerel-solaris-sparc, r-prerel-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, 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-prerel-windows-ix86+x86_64, r-prerel-linux-x86_64, r-prerel-solaris-sparc, r-prerel-solaris-x86, r-release-linux-x86_64, r-release-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-prerel-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’
    
    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, r-devel-osx-x86_64-clang, r-prerel-linux-x86_64, r-release-linux-x86_64

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-prerel-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-devel-linux-x86_64-fedora-gcc, r-prerel-windows-ix86+x86_64, r-prerel-solaris-sparc, r-prerel-solaris-x86, r-release-osx-x86_64-mavericks, r-release-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.
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of the ‘Writing R Extensions’ manual.
Flavors: r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-oldrel-windows-ix86+x86_64