Last updated on 2025-12-25 19:50:50 CET.
| Package | ERROR | OK |
|---|---|---|
| sequoia | 3 | 10 |
Current CRAN status: ERROR: 3, OK: 10
Version: 3.1.3
Check: examples
Result: ERROR
Running examples in ‘sequoia-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CalcPairLL
> ### Title: Calculate Likelihoods for Alternative Relationships
> ### Aliases: CalcPairLL
>
> ### ** Examples
>
> # Likelihoods depend on the presumed genotyping error rate:
> CalcPairLL(Pairs = data.frame(ID1='i042_2003_F', ID2='i015_2001_F'),
+ GenoM = Geno_griffin, Err = 1e-7, Plot=FALSE)
ℹ Not conditioning on any pedigree
Error in xtfrm.data.frame(list(PO = -319.07353939109, FS = -323.423047546106, :
cannot xtfrm data frames
Calls: CalcPairLL ... <Anonymous> -> .fun -> data.frame -> xtfrm -> xtfrm.data.frame
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 3.1.3
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘PedComp.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘PedComp.Rmd’
--- re-building ‘quick_start_example1.rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘quick_start_example1.rmd’
--- re-building ‘vignette-age.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘vignette-age.Rmd’
--- re-building ‘vignette-main.Rmd’ using rmarkdown
Quitting from vignette-main.Rmd:1254-1266 [griffin-useAge-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `xtfrm.data.frame()`:
! cannot xtfrm data frames
---
Backtrace:
x
1. \-sequoia::CalcPairLL(...)
2. \-plyr::adply(LLM, 1, find_bestrel)
3. \-plyr::ldply(...)
4. \-plyr::llply(...)
5. +-plyr:::loop_apply(n, do.ply)
6. \-plyr (local) `<fn>`(1L)
7. \-sequoia (local) .fun(piece, ...)
8. +-base::data.frame(...)
9. +-base::xtfrm(`<df[,7]>`)
10. \-base::xtfrm.data.frame(`<df[,7]>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'vignette-main.Rmd' failed with diagnostics:
cannot xtfrm data frames
--- failed re-building ‘vignette-main.Rmd’
--- re-building ‘flowchart.pdf.asis’ using asis
--- finished re-building ‘flowchart.pdf.asis’
--- re-building ‘vignette_mtDNA.pdf.asis’ using asis
--- finished re-building ‘vignette_mtDNA.pdf.asis’
SUMMARY: processing the following file failed:
‘vignette-main.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 3.1.3
Check: examples
Result: ERROR
Running examples in ‘sequoia-Ex.R’ failed
The error most likely occurred in:
> ### Name: CalcPairLL
> ### Title: Calculate Likelihoods for Alternative Relationships
> ### Aliases: CalcPairLL
>
> ### ** Examples
>
> # Likelihoods depend on the presumed genotyping error rate:
> CalcPairLL(Pairs = data.frame(ID1='i042_2003_F', ID2='i015_2001_F'),
+ GenoM = Geno_griffin, Err = 1e-7, Plot=FALSE)
ℹ Not conditioning on any pedigree
Error in xtfrm.data.frame(list(PO = -319.07353939109, FS = -323.423047546106, :
cannot xtfrm data frames
Calls: CalcPairLL ... <Anonymous> -> .fun -> data.frame -> xtfrm -> xtfrm.data.frame
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 3.1.3
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘PedComp.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘PedComp.Rmd’
--- re-building ‘quick_start_example1.rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘quick_start_example1.rmd’
--- re-building ‘vignette-age.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘vignette-age.Rmd’
--- re-building ‘vignette-main.Rmd’ using rmarkdown
Quitting from vignette-main.Rmd:1254-1266 [griffin-useAge-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `xtfrm.data.frame()`:
! cannot xtfrm data frames
---
Backtrace:
x
1. \-sequoia::CalcPairLL(...)
2. \-plyr::adply(LLM, 1, find_bestrel)
3. \-plyr::ldply(...)
4. \-plyr::llply(...)
5. +-plyr:::loop_apply(n, do.ply)
6. \-plyr (local) `<fn>`(1L)
7. \-sequoia (local) .fun(piece, ...)
8. +-base::data.frame(...)
9. +-base::xtfrm(`<df[,7]>`)
10. \-base::xtfrm.data.frame(`<df[,7]>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'vignette-main.Rmd' failed with diagnostics:
cannot xtfrm data frames
--- failed re-building ‘vignette-main.Rmd’
--- re-building ‘flowchart.pdf.asis’ using asis
--- finished re-building ‘flowchart.pdf.asis’
--- re-building ‘vignette_mtDNA.pdf.asis’ using asis
--- finished re-building ‘vignette_mtDNA.pdf.asis’
SUMMARY: processing the following file failed:
‘vignette-main.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc