CRAN Package Check Results for Package seqminer

Last updated on 2015-09-01 16:49:41.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 4.7 27.84 16.32 44.16 NOTE
r-devel-linux-x86_64-debian-gcc 4.7 39.62 16.36 55.98 NOTE
r-devel-linux-x86_64-fedora-clang 4.7 84.61 NOTE
r-devel-linux-x86_64-fedora-gcc 4.7 94.56 NOTE
r-devel-osx-x86_64-clang 4.7 66.77 OK
r-devel-windows-ix86+x86_64 4.7 171.00 51.00 222.00 OK
r-patched-linux-x86_64 4.7 40.85 17.00 57.85 NOTE
r-patched-solaris-sparc 4.7 487.80 ERROR
r-patched-solaris-x86 4.7 142.90 ERROR
r-release-linux-x86_64 4.7 41.32 17.18 58.50 NOTE
r-release-osx-x86_64-mavericks 4.7 NOTE
r-release-windows-ix86+x86_64 4.7 160.00 70.00 230.00 OK
r-oldrel-windows-ix86+x86_64 4.7 158.00 68.00 226.00 NOTE

Memtest notes: valgrind

Check Details

Version: 4.7
Check: installed package size
Result: NOTE
     installed size is 7.8Mb
     sub-directories of 1Mb or more:
     libs 6.6Mb
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-x86_64, r-release-osx-x86_64-mavericks

Version: 4.7
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: 4.7
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
    >
    > 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"))
    aborting ...
Flavor: r-patched-solaris-x86

Version: 4.7
Check: R code for possible problems
Result: NOTE
    download.annotation.resource: no visible global function definition for
     'dir.exists'
Flavor: r-oldrel-windows-ix86+x86_64