CRAN Package Check Results for Package seqminer

Last updated on 2020-01-23 17:49:47 CET.

Additional issues

LTO rchk

Check Details

Version: 7.1
Check: for GNU extensions in Makefiles
Result: NOTE
    GNU make is a SystemRequirements.
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-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 7.1
Check: for non-standard things in the check directory
Result: NOTE
    Found the following files/directories:
     'Makefile' 'cfh.MetaCov.assoc.gz' 'cfh.MetaCov.assoc.gz.tbi'
     'cfh.MetaScore.assoc' 'out.annotated.txt'
     'out.annotated.txt.anno.frq' 'out.annotated.txt.base.frq'
     'out.annotated.txt.codon.frq' 'out.annotated.txt.indel.frq'
     'out.annotated.txt.top.anno.frq' 'out.vcf' 'out.vcf.anno.frq'
     'out.vcf.base.frq' 'out.vcf.codon.frq' 'out.vcf.indel.frq'
     'out.vcf.top.anno.frq'
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: 7.1
Check: installed package size
Result: NOTE
     installed size is 25.9Mb
     sub-directories of 1Mb or more:
     libs 24.5Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 7.1
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
    >
    > if (.Platform$endian == "little") {
    + param <- list(reference = system.file("tabanno/test.fa", package = "seqminer"),
    + geneFile = system.file("tabanno/test.gene.txt", package = "seqminer"))
    + param <- makeAnnotationParameter(param)
    + print(param)
    + annotateGene(param, c("1", "1"), c(3, 5) , c("A", "C"), c("G", "C"))
    + } else {
    + message("Tabix does not work well for big endian for now")
    + }
    $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
    
    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