CRAN Package Check Results for Package cancerTiming

Last updated on 2014-04-21 12:43:14.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.0 0.27 1.45 1.72 ERROR
r-devel-linux-x86_64-debian-gcc 1.0.0 5.23 55.04 60.27 NOTE
r-devel-linux-x86_64-fedora-clang 1.0.0 135.69 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0.0 131.35 NOTE
r-devel-osx-x86_64-clang 1.0.0 96.94 NOTE
r-devel-osx-x86_64-gcc 1.0.0 ERROR
r-devel-windows-ix86+x86_64 1.0.0 14.00 72.00 86.00 NOTE
r-patched-linux-x86_64 1.0.0 5.24 53.06 58.30 NOTE
r-patched-solaris-sparc 1.0.0 681.60 NOTE
r-patched-solaris-x86 1.0.0 157.20 NOTE
r-release-linux-x86_64 1.0.0 5.08 53.50 58.58 NOTE
r-release-osx-x86_64-mavericks 1.0.0 ERROR
r-release-osx-x86_64-snowleopard 1.0.0 ERROR
r-release-windows-ix86+x86_64 1.0.0 18.00 100.00 118.00 NOTE
r-oldrel-windows-ix86+x86_64 1.0.0 12.00 73.00 85.00 NOTE

Check Details

Version: 1.0.0
Check: package dependencies
Result: ERROR
    Package required but not available: ‘GenomicRanges’
    
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-osx-x86_64-gcc, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard

Version: 1.0.0
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls to packages already attached by Depends:
     ‘GenomicRanges’ ‘LearnBayes’
     Please remove these calls from your code.
    Packages in Depends field not imported from:
     ‘GenomicRanges’ ‘LearnBayes’
     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-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-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.0.0
Check: R code for possible problems
Result: NOTE
    labelSeg: no visible binding for global variable ‘hg19chromosomes’
    plotAlleleByPosition: no visible binding for global variable ‘chr’
    
    Found the following calls to data() loading into the global environment:
    File ‘cancerTiming/R/labelSeg.R’:
     data(hg19chromosomes, package = "cancerTiming")
    See section ‘Good practice’ in ‘?data’.
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-osx-x86_64-clang, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.0.0
Check: Rd line widths
Result: NOTE
    Rd file 'alleleFreq.Rd':
     \usage lines wider than 90 characters:
     contAF(trueAF, totalCopy, normCont = 0, totalCopyNormal = 2, type = c("mutation", "SNPHet", "SNPHomo"))
     decontAF(contAF, totalCopy, normCont = 0, totalCopyNormal = 2, type = c("mutation", "SNPHet", "SNPHomo"))
     \examples lines wider than 100 characters:
     allAF(totalCopy=3,normCont=c(0,.1,.5),type="mutation") #allele frequencies possible for a location that is same as reference in the nor ... [TRUNCATED]
     allAF(totalCopy=3,normCont=c(0,.1,.5),type="SNPHet") #same, but for those that are heterozygous in the normal
    
    Rd file 'bootstrapEventTiming.Rd':
     \examples lines wider than 100 characters:
     x<-eventTiming(x=onlyMuts$t_alt_count,m=onlyMuts$t_depth,history=ACNLOH,totalCopy=2,type="CNLOH",normCont=0.22)
     piBoot<-bootstrapEventTiming(B=100,pi=x$pi,call=x$call,x=onlyMuts$t_alt_count,m=onlyMuts$t_depth,type="parametric")
    
    Rd file 'eventTiming.Rd':
     \usage lines wider than 90 characters:
     eventTiming(x, m, history, totalCopy, method=c("fullMLE","partialMLE","Bayes"),type=c("gain","CNLOH"),seqError=0, bootstrapCI=NULL, B=i ... [TRUNCATED]
     \examples lines wider than 100 characters:
     x<-eventTiming(x=onlyMuts$t_alt_count,m=onlyMuts$t_depth,history=ACNLOH,totalCopy=2,type="CNLOH",normCont=0.22)
    
    Rd file 'labelSeg.Rd':
     \examples lines wider than 100 characters:
     segData<-data.frame(chromosome="17",start=c(0,1.8e7+1),end=c(1.8e7,max(mutData$position)),totalCpy=c(2,NA),
    
    Rd file 'makeEventHistory.Rd':
     \usage lines wider than 90 characters:
     makeEventHistory(type = c("gain", "LOH"), copies = NULL, totalCopy = sum(copies), onlyIdentifiable = TRUE)
    
    Rd file 'mleAF.Rd':
     \examples lines wider than 100 characters:
     #note the difference in output if instead all data is from same sample (shares normal Contamination estimate)
    
    Rd file 'plotAlleleByPosition.Rd':
     \usage lines wider than 90 characters:
     plotAlleleByPosition(mutData, segmentData = NULL, whChr = 1:22, chromosomeId = "chr", sampleName = NULL, sample = FALSE, tumorAFId, pos ... [TRUNCATED]
     \examples lines wider than 100 characters:
     onlyMuts<-subset(mutData,is.na(rsID) & position <= 1.8E7) #only mutations in the CNLOH region
     segData<-data.frame(chromosome="17",start=c(0,1.8e7+1),end=c(1.8e7,max(mutData$position)),totalCpy=c(2,NA),
     out<-plotAlleleByPosition(onlyMuts,whChr=17, segmentData=segData,tCNId="totalCpy",normCont=0.22,addData=snps,pch=19,addColor="g ... [TRUNCATED]
    
    Rd file 'plotAlleleDensity.Rd':
     \usage lines wider than 90 characters:
     plotAlleleDensity(af, depth, groupingId, totalCopy, groupCol=palette(),normCont = 0,type="mutation", minDepth = 40, lineCols = c("grey" ... [TRUNCATED]
     \examples lines wider than 100 characters:
     plotAlleleDensity(onlyMuts$allelefreq,onlyMuts$t_ref_count+onlyMuts$t_alt_count,totalCopy=2,normCont=c(0,0.22),minMut=0,minDepth=0,hist ... [TRUNCATED]
     plotAlleleDensity(mutData$allelefreq,mutData$t_ref_count+mutData$t_alt_count,groupCol=c("black","red"),totalCopy=2,groupingId=gpId,minM ... [TRUNCATED]
    
    Rd file 'plotSegmentation.Rd':
     \usage lines wider than 90 characters:
     plotSegmentation(segs, valId, col = palette(),lty=1, lwd = 2, xlim, ylim,xlab="Position", ...)
     \examples lines wider than 100 characters:
     segData<-data.frame(chromosome="17",start=c(0,1.8e7+1),end=c(1.8e7,max(mutData$position)),val=c(2,3))
     out<-plotSegmentation(list(total=segData,cp1=cp1,cp2=cp2),valId="val",lwd=2,ylab="Segmentation Value")
    
    Rd file 'readSimulation.Rd':
     \usage lines wider than 90 characters:
     readSimulation(B, alleleSet, q, totalCopy, mutRate = NULL, seqError = 0, fixedN = FALSE, normCont = 0, aveReadCoverage = 30, countDistr ... [TRUNCATED]
     \examples lines wider than 100 characters:
     sims<-readSimulation(10, alleleSet=allAF(totalCopy=2)[[1]], q=qvec, totalCopy=2, mutRate = 100, seqError = 0.1, fixedN = TRUE, ... [TRUNCATED]
    
    These lines will be truncated in the PDF manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.0.0
Check: R code for possible problems
Result: NOTE
    labelSeg: no visible binding for global variable ‘hg19chromosomes’
    plotAlleleByPosition: no visible binding for global variable ‘chr’
Flavors: r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64