CRAN Package Check Results for Package cancerTiming

Last updated on 2015-03-29 09:49:07.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.0.0 0.73 12.28 13.01 ERROR
r-devel-linux-x86_64-debian-gcc 2.0.0 0.66 12.28 12.94 ERROR
r-devel-linux-x86_64-fedora-clang 2.0.0 26.32 ERROR
r-devel-linux-x86_64-fedora-gcc 2.0.0 23.77 ERROR
r-devel-osx-x86_64-clang 2.0.0 30.77 ERROR
r-prerel-windows-ix86+x86_64 2.0.0 4.00 20.00 24.00 ERROR
r-prerel-linux-x86_64 2.0.0 0.63 12.70 13.33 ERROR
r-prerel-solaris-sparc 2.0.0 133.00 ERROR
r-prerel-solaris-x86 2.0.0 33.30 ERROR
r-release-linux-x86_64 2.0.0 0.89 17.04 17.93 NOTE
r-release-osx-x86_64-mavericks 2.0.0 NOTE
r-release-osx-x86_64-snowleopard 2.0.0 OK
r-release-windows-ix86+x86_64 2.0.0 4.00 30.00 34.00 NOTE
r-oldrel-windows-ix86+x86_64 2.0.0 4.00 32.00 36.00 OK

Check Details

Version: 2.0.0
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to ‘GenomicRanges’ in package code.
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' 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-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: 2.0.0
Check: R code for possible problems
Result: NOTE
    labelSeg: no visible global function definition for ‘GRanges’
    labelSeg: no visible global function definition for ‘IRanges’
    labelSeg: no visible global function definition for ‘findOverlaps’
    labelSeg: no visible global function definition for ‘subsetByOverlaps’
    labelSeg: no visible global function definition for ‘subjectHits’
    labelSeg: no visible global function definition for ‘queryHits’
    labelSeg: no visible global function definition for ‘pintersect’
    labelSeg: no visible global function definition for ‘width’
    labelSeg: no visible global function definition for ‘values’
    labelSeg : <anonymous>: no visible global function definition for
     ‘values’
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-windows-ix86+x86_64

Version: 2.0.0
Check: examples
Result: ERROR
    Running examples in ‘cancerTiming-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: bootstrapEventTiming
    > ### Title: Bootstrap the results of eventTiming
    > ### Aliases: bootstrapEventTiming
    >
    > ### ** Examples
    >
    > ##can do this within eventTiming function, but here is an example doing it separately...
    > data(mutData)
    > ACNLOH<-matrix(c(1,3,1,0),ncol=2,nrow=2,byrow=TRUE)
    > onlyMuts<-subset(mutData,is.na(rsID) & position <= 1.8E7)
    > onlyMuts$t_depth<-onlyMuts$t_ref_count+onlyMuts$t_alt_count
    > x<-eventTiming(x=onlyMuts$t_alt_count,m=onlyMuts$t_depth,
    + history=ACNLOH,totalCopy=2,type="CNLOH",normCont=0.22,returnAssignments=TRUE)
    Error in dots[[2L]][[1L]] : object of type 'closure' is not subsettable
    Error in output$optimDetails : $ operator is invalid for atomic vectors
    Calls: eventTiming
    Execution halted
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