CRAN Package Check Results for Package seqminer

Last updated on 2014-11-24 12:47:56.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 3.1 29.68 18.05 47.73 NOTE
r-devel-linux-x86_64-debian-gcc 3.1 43.88 17.68 61.56 NOTE
r-devel-linux-x86_64-fedora-clang 3.1 102.75 NOTE
r-devel-linux-x86_64-fedora-gcc 3.1 104.99 NOTE
r-devel-osx-x86_64-clang 3.1 77.25 NOTE
r-devel-windows-ix86+x86_64 3.1 134.00 49.00 183.00 NOTE
r-patched-linux-x86_64 3.1 43.52 18.81 62.33 NOTE
r-patched-solaris-sparc 3.1 549.20 NOTE
r-patched-solaris-x86 3.1 179.90 NOTE
r-release-linux-ix86 3.1 56.78 19.00 75.79 ERROR
r-release-linux-x86_64 3.1 46.17 18.00 64.17 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 3.1 146.00 46.00 192.00 NOTE
r-oldrel-windows-ix86+x86_64 3.1 145.00 46.00 191.00 OK

Check Details

Version: 3.1
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘STARSEQ’
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-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64

Version: 3.1
Check: installed package size
Result: NOTE
     installed size is 8.9Mb
     sub-directories of 1Mb or more:
     libs 7.8Mb
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: compiled code
Result: NOTE
    File ‘seqminer/libs/seqminer.so’:
     Found ‘srand48’, possibly from ‘srand48’ (C)
     Object: ‘bcfutils.o’
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the C RNG.
    
    See ‘Writing portable 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-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64

Version: 3.1
Check: compiled code
Result: NOTE
    File ‘seqminer/libs/seqminer.so’:
     Found ‘_srand48’, possibly from ‘srand48’ (C)
     Object: ‘bcfutils.o’
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the C RNG.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavor: r-devel-osx-x86_64-clang

Version: 3.1
Check: compiled code
Result: NOTE
    File 'seqminer/libs/i386/seqminer.dll':
     Found 'rand', possibly from 'rand' (C)
     Object: 'bcfutils.o'
     Found 'srand', possibly from 'srand' (C)
     Object: 'bcfutils.o'
    File 'seqminer/libs/x64/seqminer.dll':
     Found 'rand', possibly from 'rand' (C)
     Object: 'bcfutils.o'
     Found 'srand', possibly from 'srand' (C)
     Object: 'bcfutils.o'
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the C RNG.
    
    See 'Writing portable packages' in the 'Writing R Extensions' manual.
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64

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