- using R version 4.0.0 alpha (2020-03-29 r78109)
- using platform: x86_64-apple-darwin17.0 (64-bit)
- using session charset: UTF-8
- checking for file ‘rCUR/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘rCUR’ version ‘1.3’
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘rCUR’ can be installed ... [5s/6s] OK
- checking installed package size ... OK
- checking package directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking R files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... OK
- checking whether the package can be loaded with stated dependencies ... OK
- checking whether the package can be unloaded cleanly ... OK
- checking whether the namespace can be loaded with stated dependencies ... OK
- checking whether the namespace can be unloaded cleanly ... OK
- checking loading without being on the library search path ... OK
- checking dependencies in R code ... 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.
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [3s/4s] 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').
- checking Rd files ... OK
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking examples ... 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
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [31s/46s] OK
Running ‘test01.R’ [21s/32s]
Running ‘test02.R’ [9s/14s]
- checking PDF version of manual ... OK
- DONE
Status: 1 ERROR, 2 NOTEs