CRAN Package Check Results for Package seqminer

Last updated on 2017-03-26 11:54:07.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 5.7 40.55 20.90 61.46 NOTE
r-devel-linux-x86_64-debian-gcc 5.7 43.42 20.67 64.09 NOTE
r-devel-linux-x86_64-fedora-clang 5.7 110.07 NOTE --no-stop-on-test-error
r-devel-linux-x86_64-fedora-gcc 5.7 105.42 NOTE --no-stop-on-test-error
r-devel-macos-x86_64-clang 5.7 70.04 NOTE --no-stop-on-test-error
r-devel-windows-ix86+x86_64 5.7 138.00 61.00 199.00 OK
r-patched-linux-x86_64 5.7 38.71 20.85 59.56 NOTE
r-patched-solaris-sparc 5.7 675.20 ERROR
r-patched-solaris-x86 5.7 199.60 ERROR
r-release-linux-x86_64 5.7 38.82 16.34 55.16 OK
r-release-osx-x86_64-mavericks 5.7 NOTE
r-release-windows-ix86+x86_64 5.7 183.00 53.00 236.00 OK
r-oldrel-windows-ix86+x86_64 5.7 13.00 2.00 15.00 ERROR

Memtest notes: valgrind

Check Details

Version: 5.7
Check: compiled code
Result: NOTE
    File ‘seqminer/libs/seqminer.so’:
     Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
    
    It is good practice to register native routines and to disable symbol
    search.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64

Version: 5.7
Flags: --no-stop-on-test-error
Check: installed package size
Result: NOTE
     installed size is 9.0Mb
     sub-directories of 1Mb or more:
     libs 7.8Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 5.7
Flags: --no-stop-on-test-error
Check: compiled code
Result: NOTE
    File ‘seqminer/libs/seqminer.so’:
     Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
    
    It is good practice to register native routines and to disable symbol
    search.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-x86_64-clang

Version: 5.7
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: 5.7
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"))
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86

Version: 5.7
Check: installed package size
Result: NOTE
     installed size is 8.4Mb
     sub-directories of 1Mb or more:
     libs 7.3Mb
Flavor: r-release-osx-x86_64-mavericks

Version: 5.7
Check: whether package can be installed
Result: ERROR
    Installation failed.
Flavor: r-oldrel-windows-ix86+x86_64