CRAN Package Check Results for Package seqminer

Last updated on 2018-12-14 15:51:34 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 6.7 246.89 26.40 273.29 WARN
r-devel-linux-x86_64-debian-gcc 6.7 164.62 21.15 185.77 NOTE
r-devel-linux-x86_64-fedora-clang 6.7 382.18 WARN
r-devel-linux-x86_64-fedora-gcc 6.7 291.75 NOTE
r-devel-windows-ix86+x86_64 6.7 500.00 98.00 598.00 NOTE
r-patched-linux-x86_64 6.7 197.36 24.44 221.80 NOTE
r-patched-solaris-x86 6.7 265.30 ERROR
r-release-linux-x86_64 6.7 186.45 25.01 211.46 NOTE
r-release-windows-ix86+x86_64 6.7 420.00 94.00 514.00 NOTE
r-release-osx-x86_64 6.7 WARN
r-oldrel-windows-ix86+x86_64 6.7 300.00 74.00 374.00 NOTE
r-oldrel-osx-x86_64 6.7 NOTE

Additional issues

clang-ASAN clang-UBSAN gcc-ASAN gcc-UBSAN rchk valgrind

Check Details

Version: 6.7
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: 6.7
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-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: 6.7
Check: installed package size
Result: NOTE
     installed size is 25.5Mb
     sub-directories of 1Mb or more:
     libs 24.2Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+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: 6.7
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
    >
    > 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