CRAN Package Check Results for Package seqminer

Last updated on 2017-06-29 01:47:05.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 6.0 40.84 21.40 62.24 OK
r-devel-linux-x86_64-debian-gcc 6.0 43.62 21.90 65.52 OK
r-devel-linux-x86_64-fedora-clang 6.0 108.50 NOTE
r-devel-linux-x86_64-fedora-gcc 6.0 105.58 NOTE
r-devel-windows-ix86+x86_64 6.0 133.00 58.00 191.00 OK
r-patched-linux-x86_64 6.0 43.91 20.62 64.53 OK
r-patched-solaris-sparc 6.0 623.80 ERROR
r-patched-solaris-x86 6.0 155.40 ERROR
r-release-linux-x86_64 6.0 43.09 20.67 63.75 OK
r-release-windows-ix86+x86_64 6.0 175.00 54.00 229.00 OK
r-release-osx-x86_64 6.0 NOTE
r-oldrel-windows-ix86+x86_64 6.0 161.00 73.00 234.00 OK
r-oldrel-osx-x86_64 6.0 NOTE

Additional issues

rchk

Check Details

Version: 6.0
Check: installed package size
Result: NOTE
     installed size is 9.1Mb
     sub-directories of 1Mb or more:
     libs 7.8Mb
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: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘SKAT’
Flavors: r-patched-solaris-sparc, r-patched-solaris-x86

Version: 6.0
Check: examples
Result: ERROR
    Running examples in ‘seqminer-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: tabix.read.table
    > ### Title: Read tabix file, similar to running tabix in command line.
    > ### Aliases: tabix.read.table
    >
    > ### ** Examples
    >
    > fileName = system.file("vcf/all.anno.filtered.extract.vcf.gz", package = "seqminer")
    > snp <- tabix.read.table(fileName, "1:196623337-196632470")
    [ti_index_load] wrong magic number.
    [ti_index_load] fail to load the index: /home/ripley/R/Lib32/seqminer/vcf/all.anno.filtered.extract.vcf.gz.tbi
    Cannot open specified tabix file: /home/ripley/R/Lib32/seqminer/vcf/all.anno.filtered.extract.vcf.gz
    [ti_index_load] wrong magic number.
    [ti_index_load] fail to load the index: /home/ripley/R/Lib32/seqminer/vcf/all.anno.filtered.extract.vcf.gz.tbi
    Cannot open specified tabix file: /home/ripley/R/Lib32/seqminer/vcf/all.anno.filtered.extract.vcf.gz
    Error in strsplit(body, "\t") : non-character argument
    Calls: tabix.read.table -> do.call -> strsplit
    Execution halted
Flavor: r-patched-solaris-sparc

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: .Call("annotateGene", param, chrom, position, ref, alt, PACKAGE = "seqminer")
     2: 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