CRAN Package Check Results for Package seqminer

Last updated on 2014-07-31 11:51:17.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 3.1 27.62 20.88 48.50 NOTE
r-devel-linux-x86_64-debian-gcc 3.1 43.80 19.71 63.51 NOTE
r-devel-linux-x86_64-fedora-clang 3.1 92.07 NOTE
r-devel-linux-x86_64-fedora-gcc 3.1 101.44 NOTE
r-devel-osx-x86_64-clang 3.1 82.12 OK
r-devel-windows-ix86+x86_64 3.1 148.00 47.00 195.00 OK
r-patched-linux-x86_64 3.1 43.77 20.02 63.78 NOTE
r-patched-solaris-sparc 3.1 568.00 OK
r-patched-solaris-x86 3.1 172.00 OK
r-release-linux-ix86 3.1 60.30 22.05 82.35 ERROR
r-release-linux-x86_64 3.1 46.47 20.06 66.54 NOTE
r-release-osx-x86_64-mavericks 3.1 NOTE
r-release-osx-x86_64-snowleopard 3.1 NOTE
r-release-windows-ix86+x86_64 3.1 189.00 59.00 248.00 OK
r-oldrel-windows-ix86+x86_64 3.1 124.00 52.00 176.00 OK

Check Details

Version: 3.1
Check: installed package size
Result: NOTE
     installed size is 7.8Mb
     sub-directories of 1Mb or more:
     libs 6.6Mb
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-patched-linux-x86_64, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard

Version: 3.1
Check: examples
Result: ERROR
    Running examples in seqminer-Ex.R failed
    The error most likely occurred in:
    
    > ### Name: annotateGene
    > ### Title: Annotate a test variant
    > ### Aliases: annotateGene
    >
    > ### ** Examples
    >
    > param <- list(reference = system.file("tabanno/test.fa", package = "seqminer"),
    + geneFile = system.file("tabanno/test.gene.txt", package = "seqminer"))
    > param <- makeAnnotationParameter(param)
    > print(param)
    $reference
    [1] "/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/tabanno/test.fa"
    
    $geneFile
    [1] "/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/tabanno/test.gene.txt"
    
    $geneFileFormat
    [1] "refFlat"
    
    $codonFile
    [1] "/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/tabanno/codon.txt"
    
    $priorityFile
    [1] "/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/tabanno/priority.txt"
    
    $upstreamRange
    [1] 50
    
    $downstreamRange
    [1] 50
    
    $spliceIntoExon
    [1] 3
    
    $spliceIntoIntron
    [1] 8
    
    $bed
    NULL
    
    $genomeScore
    NULL
    
    $tabix
    NULL
    
    $indexOutput
    [1] FALSE
    
    $inputFormat
    [1] "vcf"
    
    $checkReference
    [1] TRUE
    
    > annotateGene(param, c("1", "1"), c(3, 5) , c("A", "C"), c("G", "C"))
    Load reference genome /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/tabanno/test.fa...
    DONE: 1 chromosomes and 74 bases are loaded.
    Load codon file /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/tabanno/codon.txt...
    DONE: codon file loaded.
    Load priority file /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/tabanno/priority.txt...
    DONE: 25 priority annotation types loaded.
    Load gene file /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/tabanno/test.gene.txt...
    DONE: 3 gene loaded from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/tabanno/test.gene.txt.
    
     *** caught segfault ***
    address (nil), cause 'memory not mapped'
    
    Traceback:
     1: .Call("annotateGene", param, chrom, position, ref, alt, PACKAGE = "seqminer")
     2: annotateGene(param, c("1", "1"), c(3, 5), c("A", "C"), c("G", "C"))
    aborting ...
Flavor: r-release-linux-ix86