CRAN Package Check Results for Package rCUR

Last updated on 2020-04-09 09:48:23 CEST.

Check Details

Version: 1.3
Check: dependencies in R code
Result: NOTE
    Packages in Depends field not imported from:
     'MASS' 'Matrix' 'lattice' 'methods'
     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-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-linux-x86_64, r-patched-osx-x86_64, 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: 1.3
Check: R code for possible problems
Result: NOTE
    CUR: no visible global function definition for 'runif'
    CUR: no visible global function definition for 'new'
    plotLeverage,CURobj: no visible global function definition for 'points'
    plotLeverage,CURobj: no visible global function definition for 'abline'
    Undefined global functions or variables:
     abline new points runif
    Consider adding
     importFrom("graphics", "abline", "points")
     importFrom("methods", "new")
     importFrom("stats", "runif")
    to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
    contains 'methods').
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-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-linux-x86_64, r-patched-osx-x86_64, r-patched-solaris-x86

Version: 1.3
Check: examples
Result: ERROR
    Running examples in 'rCUR-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: rCUR-package
    > ### Title: CUR matrix decomposition package
    > ### Aliases: rCUR-package rCUR
    > ### Keywords: svd prcomp
    >
    > ### ** Examples
    >
    > library(rCUR)
    > library(lattice)
    >
    > data(STTm)
    > data(STTa)
    >
    > n = 27
    > res = CUR(STTm, 31, n, 4)
    >
    > plotLeverage(res, C=FALSE, top.n=n, xlab='Gene ID', las=1, top.col='black',
    + top.pch=16, ul.col='black', ul.lty=2, col='grey')
    >
    > PCA01 = prcomp(STTm, scale=TRUE)
    >
    > top.idx = topLeverage(res, C=FALSE, top.n=n, sort=FALSE)
    > top.STTm = STTm[top.idx,]
    > PCA02 = prcomp(top.STTm, scale=TRUE)
    >
    > t.top.STTm = t(top.STTm)
    > x = 1:dim(t.top.STTm)[1]
    > y = 1:dim(t.top.STTm)[2]
    >
    > ann.tab = STTa[top.idx,]
    > genes = as.character(ann.tab$Gene)
    > genes[genes==''] = as.character(ann.tab[genes=='','Hs'])
    >
    > op = par(mar=c(3.5, 0, 0, 5) + 0.1)
    > image(x, y, t.top.STTm, col=rev(gray(0:256/300)), axes=FALSE, xlab='',
    + ylab='')
    > axis(1, at=c(10,22,31), labels=c('GIST','LEIO','SARC'), tick=FALSE,
    + las=2, cex=0.6, line=-0.8)
    > axis(4, at=1:length(genes), labels=genes, tick=FALSE, las=1, cex=0.6,
    + line=-0.8)
    > par(op)
    >
    > PCAs = rbind(PCA01$rotation[,c(1,2)], PCA02$rotation[,c(1,2)])
    > group = rownames(PCAs)
    > pchs = ifelse(group=='GIST', 16, 0)
    > pchs = ifelse(group=='LEIO', 17, pchs)
    > pchs = ifelse(group=='SARC', 18, pchs)
    > PCAs = data.frame(PC1=PCAs[,1], PC2=PCAs[,2],
    + lab=c(rep('all',31),rep('selected',31)), group, pchs)
    >
    > xyplot(PC2 ~ PC1 | lab, data = PCAs, pch=pchs, cex=1.0, col='black',
    + fill='black', key = list(space = "bottom", text = list(levels(PCAs$group)),
    + points=TRUE, pch=c(16, 17, 18), fill='black', columns=3, just=1))
    Error in fun(key = base::quote(list(space = "bottom", text = list(NULL), :
     first component of text must be vector of labels
    Calls: <Anonymous> ... print.trellis -> printFunction -> evaluate.legend -> do.call -> fun
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64

Version: 1.3
Check: examples
Result: ERROR
    Running examples in ‘rCUR-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: rCUR-package
    > ### Title: CUR matrix decomposition package
    > ### Aliases: rCUR-package rCUR
    > ### Keywords: svd prcomp
    >
    > ### ** Examples
    >
    > library(rCUR)
    > library(lattice)
    >
    > data(STTm)
    > data(STTa)
    >
    > n = 27
    > res = CUR(STTm, 31, n, 4)
    >
    > plotLeverage(res, C=FALSE, top.n=n, xlab='Gene ID', las=1, top.col='black',
    + top.pch=16, ul.col='black', ul.lty=2, col='grey')
    >
    > PCA01 = prcomp(STTm, scale=TRUE)
    >
    > top.idx = topLeverage(res, C=FALSE, top.n=n, sort=FALSE)
    > top.STTm = STTm[top.idx,]
    > PCA02 = prcomp(top.STTm, scale=TRUE)
    >
    > t.top.STTm = t(top.STTm)
    > x = 1:dim(t.top.STTm)[1]
    > y = 1:dim(t.top.STTm)[2]
    >
    > ann.tab = STTa[top.idx,]
    > genes = as.character(ann.tab$Gene)
    > genes[genes==''] = as.character(ann.tab[genes=='','Hs'])
    >
    > op = par(mar=c(3.5, 0, 0, 5) + 0.1)
    > image(x, y, t.top.STTm, col=rev(gray(0:256/300)), axes=FALSE, xlab='',
    + ylab='')
    > axis(1, at=c(10,22,31), labels=c('GIST','LEIO','SARC'), tick=FALSE,
    + las=2, cex=0.6, line=-0.8)
    > axis(4, at=1:length(genes), labels=genes, tick=FALSE, las=1, cex=0.6,
    + line=-0.8)
    > par(op)
    >
    > PCAs = rbind(PCA01$rotation[,c(1,2)], PCA02$rotation[,c(1,2)])
    > group = rownames(PCAs)
    > pchs = ifelse(group=='GIST', 16, 0)
    > pchs = ifelse(group=='LEIO', 17, pchs)
    > pchs = ifelse(group=='SARC', 18, pchs)
    > PCAs = data.frame(PC1=PCAs[,1], PC2=PCAs[,2],
    + lab=c(rep('all',31),rep('selected',31)), group, pchs)
    >
    > xyplot(PC2 ~ PC1 | lab, data = PCAs, pch=pchs, cex=1.0, col='black',
    + fill='black', key = list(space = "bottom", text = list(levels(PCAs$group)),
    + points=TRUE, pch=c(16, 17, 18), fill='black', columns=3, just=1))
    Error in fun(key = base::quote(list(space = "bottom", text = list(NULL), :
     first component of text must be vector of labels
    Calls: <Anonymous> ... print.trellis -> printFunction -> evaluate.legend -> do.call -> fun
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-osx-x86_64, r-patched-solaris-x86

Version: 1.3
Check: R code for possible problems
Result: NOTE
    CUR: no visible global function definition for ‘runif’
    CUR: no visible global function definition for ‘new’
    plotLeverage,CURobj: no visible global function definition for ‘plot’
    plotLeverage,CURobj: no visible global function definition for ‘points’
    plotLeverage,CURobj: no visible global function definition for ‘abline’
    Undefined global functions or variables:
     abline new plot points runif
    Consider adding
     importFrom("graphics", "abline", "plot", "points")
     importFrom("methods", "new")
     importFrom("stats", "runif")
    to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
    contains 'methods').
Flavors: 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