Last updated on 2019-01-07 08:00:54 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 9.63 | 77.17 | 86.80 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 8.92 | 57.75 | 66.67 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 51.60 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 92.41 | NOTE | |||
| r-devel-windows-ix86+x86_64 | 1.1.0 | 28.00 | 149.00 | 177.00 | OK | |
| r-patched-linux-x86_64 | 1.1.0 | 10.89 | 70.01 | 80.90 | NOTE | |
| r-patched-solaris-x86 | 1.1.0 | 173.60 | NOTE | |||
| r-release-linux-x86_64 | 1.1.0 | 11.55 | 69.29 | 80.84 | NOTE | |
| r-release-windows-ix86+x86_64 | 1.1.0 | 23.00 | 164.00 | 187.00 | OK | |
| r-release-osx-x86_64 | 1.1.0 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 1.1.0 | 18.00 | 192.00 | 210.00 | OK | |
| r-oldrel-osx-x86_64 | 1.1.0 | OK |
Version: 1.1.0
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘GenABEL’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64
Version: 1.1.0
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking: 'GenABEL', 'seqminer'
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.1.0
Check: examples
Result: ERROR
Running examples in ‘FREGAT-Ex.R’ failed
The error most likely occurred in:
> ### Name: FFBSKAT
> ### Title: Fast Family-Based SKAT, SKAT-O
> ### Aliases: FFBSKAT
>
> ### ** Examples
>
>
> data(example.data)
>
> ## Run FFBSKAT with sliding window (default):
> out <- FFBSKAT(trait ~ age + sex, phenodata, genodata, kin)
>
> ## Run FFBSKAT with regions defined in snpdata$gene and with
> ## null model obtained in first run:
> out <- FFBSKAT(trait ~ age + sex, phenodata, genodata, kin,
+ out$nullmod, regions = snpdata$gene)
>
> ## Run FFBSKAT parallelized on two cores (this will require
> ## 'foreach' and 'doParallel' R-packages installed and
> ## cores available):
> out <- FFBSKAT(trait ~ age + sex, phenodata, genodata, kin,
+ out$nullmod, ncores = 2)
>
> ## Run FFBSKAT with genotypes in VCF format:
> VCFfileName <- system.file(
+ "testfiles/1000g.phase1.20110521.CFH.var.anno.vcf.gz",
+ package = "FREGAT")
> geneFile <- system.file("testfiles/refFlat_hg19_6col.txt.gz",
+ package = "FREGAT")
> phe <- data.frame(trait = rnorm(85))
> out <- FFBSKAT(trait, phe, VCFfileName, geneFile = geneFile,
+ reg = "CFH", annoType = "Nonsynonymous",
+ flip.genotypes = TRUE)
Error in check.geno(genodata, regions, n, ...) :
Please install 'seqminer' package to process VCF file
Calls: FFBSKAT -> do.call -> <Anonymous> -> check.geno
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang