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 |
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