Last updated on 2023-04-27 14:53:11 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.0 | 3.01 | 34.11 | 37.12 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 0.2.0 | 2.61 | 26.55 | 29.16 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 0.2.0 | 49.97 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 0.2.0 | 56.05 | NOTE | |||
| r-devel-windows-x86_64 | 0.2.0 | 12.00 | 76.00 | 88.00 | ERROR | |
| r-patched-linux-x86_64 | 0.2.0 | 3.21 | 33.44 | 36.65 | NOTE | |
| r-release-linux-x86_64 | 0.2.0 | 3.12 | 33.03 | 36.15 | NOTE | |
| r-release-macos-arm64 | 0.2.0 | 25.00 | OK | |||
| r-release-macos-x86_64 | 0.2.0 | 38.00 | OK | |||
| r-release-windows-x86_64 | 0.2.0 | 8.00 | 65.00 | 73.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.2.0 | 21.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.2.0 | 27.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.2.0 | 5.00 | 61.00 | 66.00 | OK |
Version: 0.2.0
Check: for non-standard things in the check directory
Result: NOTE
Found the following files/directories:
‘simu.pheno’ ‘usedpars.txt’
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-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.2.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'SimPhe.Rmd' using rmarkdown
Quitting from lines 77-83 (SimPhe.Rmd)
Error: processing vignette 'SimPhe.Rmd' failed with diagnostics:
'data' must be of a vector type, was 'NULL'
--- failed re-building 'SimPhe.Rmd'
SUMMARY: processing the following file failed:
'SimPhe.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64
Version: 0.2.0
Check: examples
Result: ERROR
Running examples in 'SimPhe-Ex.R' failed
The error most likely occurred in:
> ### Name: sim.phe
> ### Title: Simulation for phenotypes (SimPhe main process)
> ### Aliases: sim.phe
>
> ### ** Examples
>
> #### file path of example
> # simulation parameters:
> fpar.path <- system.file("extdata", "simupars.txt", package="SimPhe")
>
> # genotype file: rows are individuals and columns are SNPs
> fgeno.path <- system.file("extdata", "10SNP.txt", package="SimPhe")
>
>
> #### instead of a parameter file, prepared list like genepars also works
> genepars
$P1mean
mean
1 10
$P1main
SNP additive dominance
1 SNP01 4.0 2.0
2 SNP02 2.5 1.5
3 SNP03 5.5 1.8
4 SNP04 -2.5 1.0
5 SNP05 8.5 9.8
6 SNP06 8.7 8.4
$P1epistasis
SNPA SNPB additive_additive additive_dominance dominance_additive
1 SNP01 SNP02 10.0 2.0 2.8
2 SNP03 SNP04 8.0 3.0 3.5
3 SNP05 SNP06 20.5 20.6 20.4
dominance_dominance
1 1.8
2 2.5
3 10.2
$P1heritability
heritability
1 0.6
$P2mean
mean
1 20
$P2main
SNP additive dominance
1 SNP01 8.0 2.0
2 SNP02 4.5 1.8
3 SNP03 6.5 1.5
4 SNP04 -3.5 -1.2
5 SNP07 10.4 8.6
6 SNP08 12.3 11.9
$P2epistasis
SNPA SNPB additive_additive additive_dominance dominance_additive
1 SNP01 SNP02 15.0 4.0 3.0
2 SNP03 SNP04 12.0 5.0 3.5
3 SNP07 SNP08 21.5 20.9 20.5
dominance_dominance
1 2.0
2 2.5
3 20.3
>
>
> #### simulate phenotype(s)
> phe <- sim.phe(sim.pars = fpar.path, fgeno = fgeno.path, ftype = "snp.head", fwrite = FALSE)
Warning in readLines(file.new) :
line 1 appears to contain an embedded nul
Warning in readLines(file.new) :
line 2 appears to contain an embedded nul
Warning in readLines(file.new) :
line 3 appears to contain an embedded nul
Warning in readLines(file.new) :
line 4 appears to contain an embedded nul
Warning in readLines(file.new) :
line 5 appears to contain an embedded nul
Warning in readLines(file.new) :
line 6 appears to contain an embedded nul
Warning in readLines(file.new) :
line 7 appears to contain an embedded nul
Warning in readLines(file.new) :
line 8 appears to contain an embedded nul
Warning in readLines(file.new) :
line 9 appears to contain an embedded nul
Warning in readLines(file.new) :
line 10 appears to contain an embedded nul
Warning in readLines(file.new) :
line 11 appears to contain an embedded nul
Warning in readLines(file.new) :
line 12 appears to contain an embedded nul
Warning in readLines(file.new) :
line 13 appears to contain an embedded nul
Warning in readLines(file.new) :
line 14 appears to contain an embedded nul
Warning in readLines(file.new) :
line 15 appears to contain an embedded nul
Warning in readLines(file.new) :
line 16 appears to contain an embedded nul
Warning in readLines(file.new) :
line 17 appears to contain an embedded nul
Warning in readLines(file.new) :
line 18 appears to contain an embedded nul
Warning in readLines(file.new) :
line 19 appears to contain an embedded nul
Warning in readLines(file.new) :
line 20 appears to contain an embedded nul
Warning in readLines(file.new) :
line 21 appears to contain an embedded nul
Warning in readLines(file.new) :
line 22 appears to contain an embedded nul
Warning in readLines(file.new) :
line 23 appears to contain an embedded nul
Warning in readLines(file.new) :
line 24 appears to contain an embedded nul
Warning in readLines(file.new) :
line 25 appears to contain an embedded nul
Warning in readLines(file.new) :
line 26 appears to contain an embedded nul
Warning in readLines(file.new) :
line 27 appears to contain an embedded nul
Warning in readLines(file.new) :
line 28 appears to contain an embedded nul
Warning in readLines(file.new) :
line 29 appears to contain an embedded nul
Warning in readLines(file.new) :
line 30 appears to contain an embedded nul
Warning in readLines(file.new) :
line 31 appears to contain an embedded nul
Warning in readLines(file.new) :
line 32 appears to contain an embedded nul
Warning in readLines(file.new) :
line 33 appears to contain an embedded nul
Warning in readLines(file.new) :
line 34 appears to contain an embedded nul
Warning in readLines(file.new) :
line 35 appears to contain an embedded nul
Warning in readLines(file.new) :
line 36 appears to contain an embedded nul
Warning in grep("^\\[", all.lines) :
unable to translate '<ef>[' to a wide string
Warning in grep("^\\[", all.lines) : input string 1 is invalid
Error in matrix(unlist(sapply(regmatches(x, gregexpr(pattern, x)), function(e) regmatches(e, :
'data' must be of a vector type, was 'NULL'
Calls: sim.phe -> read.simu.pars -> regextract -> matrix
Execution halted
Flavor: r-release-windows-x86_64