CRAN Package Check Results for Package detectRUNS

Last updated on 2018-08-20 09:47:34 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.9.5 22.55 76.96 99.51 OK
r-devel-linux-x86_64-debian-gcc 0.9.5 22.55 60.06 82.61 OK
r-devel-linux-x86_64-fedora-clang 0.9.5 125.25 OK
r-devel-linux-x86_64-fedora-gcc 0.9.5 119.44 OK
r-devel-windows-ix86+x86_64 0.9.5 62.00 184.00 246.00 ERROR
r-patched-linux-x86_64 0.9.5 24.84 71.21 96.05 OK
r-patched-solaris-x86 0.9.5 150.50 OK
r-release-linux-x86_64 0.9.5 26.32 70.86 97.18 OK
r-release-windows-ix86+x86_64 0.9.5 62.00 174.00 236.00 OK
r-release-osx-x86_64 0.9.5 OK
r-oldrel-windows-ix86+x86_64 0.9.5 46.00 197.00 243.00 OK
r-oldrel-osx-x86_64 0.9.5 OK

Check Details

Version: 0.9.5
Check: running examples for arch ‘i386’
Result: ERROR
    Running examples in 'detectRUNS-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: tableRuns
    > ### Title: Function to retrieve most common runs in the population
    > ### Aliases: tableRuns
    >
    > ### ** Examples
    >
    > # getting map and ped paths
    > genotypeFile <- system.file("extdata", "Kijas2016_Sheep_subset.ped", package = "detectRUNS")
    > mapFile <- system.file("extdata", "Kijas2016_Sheep_subset.map", package = "detectRUNS")
    >
    > # calculating runs of Homozygosity
    > ## Not run:
    > ##D # skipping runs calculation
    > ##D runs <- slidingRUNS.run(genotypeFile, mapFile, windowSize = 15, threshold = 0.1, minSNP = 15,
    > ##D ROHet = FALSE, maxOppositeGenotype = 1, maxMiss = 1, minLengthBps = 100000, minDensity = 1/10000)
    > ## End(Not run)
    > # loading pre-calculated data
    > runsFile <- system.file("extdata", "Kijas2016_Sheep_subset.sliding.csv", package="detectRUNS")
    > runsDF = readExternalRuns(inputFile = runsFile, program = 'detectRUNS')
    Loading file from detectRUNS
    >
    > tableRuns(runs = runsDF, genotypeFile = genotypeFile, mapFile = mapFile, threshold = 0.5)
    Threshold used: 50
    I found only Runs data frame. GOOD!
    Calculation % SNP in ROH
    Chromosome founds: 2
    
     |
     | | 0%
     |
     |=================================== | 50%
     |
     |======================================================================| 100%
    Calculation % SNP in ROH finish
    checking: Jacobs
    checking: Navajo-Churro
     Group Start_SNP End_SNP chrom nSNP from to
    1 Jacobs OAR2_2415898.1 OAR2_2415898.1 2 1 4166902 4166902
    2 Jacobs OAR2_58221964.1 OAR2_58845032.1 2 13 54135888 54687816
    3 Jacobs s63709.1 OAR2_76435176.1 2 19 70664942 71739429
    4 Jacobs OAR2_77896643.1 OAR2_78825486.1 2 16 73109758 73926990
    5 Jacobs OAR2_130215973.1 OAR2_131783123.1 2 24 121796989 123573014
    6 Jacobs OAR2_227848218.1 s09037.1 2 6 215443702 215641893
    7 Jacobs s52064.1 OAR2_229781196.1 2 7 215844761 217457102
    8 Jacobs s72964.1 s53910.1 2 18 217719922 219015064
    9 Jacobs s50915.1 OAR2_232672067.1 2 2 220083076 220103004
    10 Jacobs s07830.1 s41614.1 24 12 16041579 17133716
    >
    >
    >
    >
    > ### * <FOOTER>
    > ###
    > cleanEx()
    Error: connections left open:
     gsub("[,\\; \t]", "\t", readLines(inputFile)) (textConnection)
    Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 0.9.5
Check: running examples for arch ‘x64’
Result: ERROR
    Running examples in 'detectRUNS-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: tableRuns
    > ### Title: Function to retrieve most common runs in the population
    > ### Aliases: tableRuns
    >
    > ### ** Examples
    >
    > # getting map and ped paths
    > genotypeFile <- system.file("extdata", "Kijas2016_Sheep_subset.ped", package = "detectRUNS")
    > mapFile <- system.file("extdata", "Kijas2016_Sheep_subset.map", package = "detectRUNS")
    >
    > # calculating runs of Homozygosity
    > ## Not run:
    > ##D # skipping runs calculation
    > ##D runs <- slidingRUNS.run(genotypeFile, mapFile, windowSize = 15, threshold = 0.1, minSNP = 15,
    > ##D ROHet = FALSE, maxOppositeGenotype = 1, maxMiss = 1, minLengthBps = 100000, minDensity = 1/10000)
    > ## End(Not run)
    > # loading pre-calculated data
    > runsFile <- system.file("extdata", "Kijas2016_Sheep_subset.sliding.csv", package="detectRUNS")
    > runsDF = readExternalRuns(inputFile = runsFile, program = 'detectRUNS')
    Loading file from detectRUNS
    >
    > tableRuns(runs = runsDF, genotypeFile = genotypeFile, mapFile = mapFile, threshold = 0.5)
    Threshold used: 50
    I found only Runs data frame. GOOD!
    Calculation % SNP in ROH
    Chromosome founds: 2
    
     |
     | | 0%
     |
     |=================================== | 50%
     |
     |======================================================================| 100%
    Calculation % SNP in ROH finish
    checking: Jacobs
    checking: Navajo-Churro
     Group Start_SNP End_SNP chrom nSNP from to
    1 Jacobs OAR2_2415898.1 OAR2_2415898.1 2 1 4166902 4166902
    2 Jacobs OAR2_58221964.1 OAR2_58845032.1 2 13 54135888 54687816
    3 Jacobs s63709.1 OAR2_76435176.1 2 19 70664942 71739429
    4 Jacobs OAR2_77896643.1 OAR2_78825486.1 2 16 73109758 73926990
    5 Jacobs OAR2_130215973.1 OAR2_131783123.1 2 24 121796989 123573014
    6 Jacobs OAR2_227848218.1 s09037.1 2 6 215443702 215641893
    7 Jacobs s52064.1 OAR2_229781196.1 2 7 215844761 217457102
    8 Jacobs s72964.1 s53910.1 2 18 217719922 219015064
    9 Jacobs s50915.1 OAR2_232672067.1 2 2 220083076 220103004
    10 Jacobs s07830.1 s41614.1 24 12 16041579 17133716
    >
    >
    >
    >
    > ### * <FOOTER>
    > ###
    > cleanEx()
    Error: connections left open:
     gsub("[,\\; \t]", "\t", readLines(inputFile)) (textConnection)
    Execution halted
Flavor: r-devel-windows-ix86+x86_64