CRAN Package Check Results for Package seqminer

Last updated on 2018-04-24 19:54:40 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 6.0 69.46 22.92 92.38 WARN
r-devel-linux-x86_64-debian-gcc 6.0 56.03 18.44 74.47 OK
r-devel-linux-x86_64-fedora-clang 6.0 114.36 WARN
r-devel-linux-x86_64-fedora-gcc 6.0 106.59 NOTE
r-devel-windows-ix86+x86_64 6.0 186.00 69.00 255.00 OK
r-patched-linux-x86_64 6.0 68.46 22.68 91.14 OK
r-patched-solaris-x86 6.0 161.40 ERROR
r-release-linux-x86_64 6.0 67.74 22.33 90.07 OK
r-release-windows-ix86+x86_64 6.0 186.00 69.00 255.00 OK
r-release-osx-x86_64 6.0 WARN
r-oldrel-windows-ix86+x86_64 6.0 143.00 83.00 226.00 OK
r-oldrel-osx-x86_64 6.0 NOTE

Check Details

Version: 6.0
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     vcf.c:253:15: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-fedora-clang, r-release-osx-x86_64

Version: 6.0
Check: installed package size
Result: NOTE
     installed size is 9.5Mb
     sub-directories of 1Mb or more:
     libs 8.2Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 6.0
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/ripley/R/Lib32/seqminer/tabanno/test.fa"
    
    $geneFile
    [1] "/home/ripley/R/Lib32/seqminer/tabanno/test.gene.txt"
    
    $geneFileFormat
    [1] "refFlat"
    
    $codonFile
    [1] "/home/ripley/R/Lib32/seqminer/tabanno/codon.txt"
    
    $priorityFile
    [1] "/home/ripley/R/Lib32/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/ripley/R/Lib32/seqminer/tabanno/test.fa...
    DONE: 1 chromosomes and 74 bases are loaded.
    Load codon file /home/ripley/R/Lib32/seqminer/tabanno/codon.txt...
    DONE: codon file loaded.
    Load priority file /home/ripley/R/Lib32/seqminer/tabanno/priority.txt...
    DONE: 25 priority annotation types loaded.
    Load gene file /home/ripley/R/Lib32/seqminer/tabanno/test.gene.txt...
    DONE: 3 gene loaded from /home/ripley/R/Lib32/seqminer/tabanno/test.gene.txt.
    
     *** caught segfault ***
    address 0, cause 'memory not mapped'
    
    Traceback:
     1: annotateGene(param, c("1", "1"), c(3, 5), c("A", "C"), c("G", "C"))
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86