CRAN Package Check Results for Package seqminer

Last updated on 2014-04-20 17:47:05.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 3.0 31.72 22.77 54.48 NOTE
r-devel-linux-x86_64-debian-gcc 3.0 41.81 23.78 65.58 NOTE
r-devel-linux-x86_64-fedora-clang 3.0 61.61 NOTE
r-devel-linux-x86_64-fedora-gcc 3.0 103.00 NOTE
r-devel-macosx-x86_64-clang 3.0 35.65 OK
r-devel-macosx-x86_64-gcc 2.7 OK
r-devel-windows-ix86+x86_64 2.7 141.00 44.00 185.00 OK
r-patched-linux-x86_64 2.7 42.78 21.62 64.40 WARN
r-patched-solaris-sparc 3.0 505.60 OK
r-patched-solaris-x86 3.0 142.10 OK
r-release-linux-ix86 ERROR
r-release-linux-x86_64 2.7 41.65 21.35 63.00 WARN
r-release-macosx-x86_64 2.7 OK
r-release-windows-ix86+x86_64 3.0 120.00 44.00 164.00 OK
r-oldrel-windows-ix86+x86_64 3.0 115.00 53.00 168.00 OK

Check Details

Version: 3.0
Check: installed package size
Result: NOTE
     installed size is 8.0Mb
     sub-directories of 1Mb or more:
     libs 6.8Mb
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

Version: 2.7
Check: whether package can be installed
Result: WARNING
    Found the following significant warnings:
     StringUtil.h:216:33: warning: ISO C++98 does not support the ‘%lf’ gnu_printf format [-Wformat=]
     StringUtil.h:216:33: warning: ISO C++98 does not support the ‘%lf’ gnu_printf format [-Wformat=]
     StringUtil.h:216:33: warning: ISO C++98 does not support the ‘%lf’ gnu_printf format [-Wformat=]
     StringUtil.h:216:33: warning: ISO C++98 does not support the ‘%lf’ gnu_printf format [-Wformat=]
     StringUtil.h:216:33: warning: ISO C++98 does not support the ‘%lf’ gnu_printf format [-Wformat=]
     StringUtil.h:216:33: warning: ISO C++98 does not support the ‘%lf’ gnu_printf format [-Wformat=]
     StringUtil.h:216:33: warning: ISO C++98 does not support the ‘%lf’ gnu_printf format [-Wformat=]
     StringUtil.h:216:33: warning: ISO C++98 does not support the ‘%lf’ gnu_printf format [-Wformat=]
     StringUtil.h:216:33: warning: ISO C++98 does not support the ‘%lf’ gnu_printf format [-Wformat=]
     StringUtil.h:216:33: warning: ISO C++98 does not support the ‘%lf’ gnu_printf format [-Wformat=]
     StringUtil.h:216:33: warning: ISO C++98 does not support the ‘%lf’ gnu_printf format [-Wformat=]
     StringUtil.h:216:33: warning: ISO C++98 does not support the ‘%lf’ gnu_printf format [-Wformat=]
     StringUtil.h:216:33: warning: ISO C++98 does not support the ‘%lf’ gnu_printf format [-Wformat=]
     StringUtil.h:216:33: warning: ISO C++98 does not support the ‘%lf’ gnu_printf format [-Wformat=]
    See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/seqminer.Rcheck/00install.out’ for details.
Flavor: r-patched-linux-x86_64

Version: 2.7
Check: installed package size
Result: NOTE
     installed size is 9.5Mb
     sub-directories of 1Mb or more:
     libs 8.3Mb
Flavors: r-patched-linux-x86_64, r-release-linux-ix86, r-release-linux-x86_64

Version: 2.7
Check: whether package can be installed
Result: WARNING
    Found the following significant warnings:
     StringUtil.h:216:33: warning: ISO C++98 does not support the ‘%lf’ gnu_printf format [-Wformat=]
     StringUtil.h:216:33: warning: ISO C++98 does not support the ‘%lf’ gnu_printf format [-Wformat=]
     StringUtil.h:216:33: warning: ISO C++98 does not support the ‘%lf’ gnu_printf format [-Wformat=]
     StringUtil.h:216:33: warning: ISO C++98 does not support the ‘%lf’ gnu_printf format [-Wformat=]
     StringUtil.h:216:33: warning: ISO C++98 does not support the ‘%lf’ gnu_printf format [-Wformat=]
     StringUtil.h:216:33: warning: ISO C++98 does not support the ‘%lf’ gnu_printf format [-Wformat=]
     StringUtil.h:216:33: warning: ISO C++98 does not support the ‘%lf’ gnu_printf format [-Wformat=]
     StringUtil.h:216:33: warning: ISO C++98 does not support the ‘%lf’ gnu_printf format [-Wformat=]
     StringUtil.h:216:33: warning: ISO C++98 does not support the ‘%lf’ gnu_printf format [-Wformat=]
     StringUtil.h:216:33: warning: ISO C++98 does not support the ‘%lf’ gnu_printf format [-Wformat=]
     StringUtil.h:216:33: warning: ISO C++98 does not support the ‘%lf’ gnu_printf format [-Wformat=]
     StringUtil.h:216:33: warning: ISO C++98 does not support the ‘%lf’ gnu_printf format [-Wformat=]
     StringUtil.h:216:33: warning: ISO C++98 does not support the ‘%lf’ gnu_printf format [-Wformat=]
     StringUtil.h:216:33: warning: ISO C++98 does not support the ‘%lf’ gnu_printf format [-Wformat=]
    See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/seqminer.Rcheck/00install.out’ for details.
Flavors: r-release-linux-ix86, r-release-linux-x86_64

Version: 2.7
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
    >
    > reference = system.file("tabanno/test.fa", package = "seqminer")
    > refBase <- getRefBase(reference, chrom = c(1, 1), pos = c(1, 2), len = c(1, 1))
    to open /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/tabanno/test.fa
    >
    > 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
    
    > 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