Last updated on 2020-04-09 09:48:25 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.6 | 5.78 | 148.31 | 154.09 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 2.0.6 | 5.43 | 112.99 | 118.42 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.0.6 | 178.81 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.6 | 186.45 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 2.0.6 | 13.00 | 200.00 | 213.00 | ERROR | |
| r-devel-windows-ix86+x86_64-gcc8 | 2.0.6 | 12.00 | 143.00 | 155.00 | ERROR | |
| r-patched-linux-x86_64 | 2.0.6 | 6.65 | 141.97 | 148.62 | ERROR | |
| r-patched-osx-x86_64 | 2.0.6 | ERROR | ||||
| r-patched-solaris-x86 | 2.0.6 | 231.90 | ERROR | |||
| r-release-linux-x86_64 | 2.0.6 | 5.03 | 157.94 | 162.97 | OK | |
| r-release-windows-ix86+x86_64 | 2.0.6 | 13.00 | 184.00 | 197.00 | OK | |
| r-release-osx-x86_64 | 2.0.6 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 2.0.6 | 15.00 | 140.00 | 155.00 | OK | |
| r-oldrel-osx-x86_64 | 2.0.6 | OK |
Version: 2.0.6
Check: examples
Result: ERROR
Running examples in 'rtrim-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: index
> ### Title: Extract time-indices from TRIM output.
> ### Aliases: index
>
> ### ** Examples
>
>
> data(skylark)
> z <- trim(count ~ site + time, data=skylark, model=2)
> index(z)
time imputed se_imp
1 1 1.0000000 0.00000000
2 2 0.8955586 0.03961601
3 3 0.9871129 0.05149670
4 4 0.9907025 0.05617083
5 5 1.0841256 0.06472818
6 6 1.1902220 0.07523418
7 7 1.2715570 0.08597312
8 8 1.3498571 0.09976989
> # mimic classic TRIM:
> index(z, "both")
time fitted se_fit imputed se_imp
1 1 1.000000 0.00000000 1.0000000 0.00000000
2 2 1.056356 0.01102452 0.8955586 0.03961601
3 3 1.115888 0.02329164 0.9871129 0.05149670
4 4 1.178776 0.03690640 0.9907025 0.05617083
5 5 1.245207 0.05198174 1.0841256 0.06472818
6 6 1.315382 0.06863904 1.1902220 0.07523418
7 7 1.389512 0.08700873 1.2715570 0.08597312
8 8 1.467820 0.10723092 1.3498571 0.09976989
> # Extract standard errors for the imputed data
> SE <- index(z,"imputed")$se_mod
> # Include covariates
> skylark$Habitat <- factor(skylark$Habitat) # hack
> z <- trim(count ~ site + time + Habitat, data=skylark, model=2)
> ind <- index(z, covars=TRUE)
> plot(ind)
Error in if (!covar %in% levels(z$covariate)) stop(sprintf("Covariate \"%s\" not present in index data", :
argument is of length zero
Calls: plot -> plot.trim.index
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64
Version: 2.0.6
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'Skylark_example.Rmd' using rmarkdown
Quitting from lines 171-172 (Skylark_example.Rmd)
Error: processing vignette 'Skylark_example.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'Skylark_example.Rmd'
--- re-building 'rtrim_2_extensions.Rmd' using rmarkdown
Quitting from lines 261-264 (rtrim_2_extensions.Rmd)
Error: processing vignette 'rtrim_2_extensions.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'rtrim_2_extensions.Rmd'
--- re-building 'rtrim_confidence_intervals.Rmd' using rmarkdown
--- finished re-building 'rtrim_confidence_intervals.Rmd'
--- re-building 'rtrim_for_TRIM_users.Rmd' using rmarkdown
--- finished re-building 'rtrim_for_TRIM_users.Rmd'
--- re-building 'taming_overdispersion.Rmd' using rmarkdown
--- finished re-building 'taming_overdispersion.Rmd'
--- re-building 'TRIM_methods_v2.pdf.asis' using asis
--- finished re-building 'TRIM_methods_v2.pdf.asis'
SUMMARY: processing the following files failed:
'Skylark_example.Rmd' 'rtrim_2_extensions.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64
Version: 2.0.6
Check: examples
Result: ERROR
Running examples in ‘rtrim-Ex.R’ failed
The error most likely occurred in:
> ### Name: index
> ### Title: Extract time-indices from TRIM output.
> ### Aliases: index
>
> ### ** Examples
>
>
> data(skylark)
> z <- trim(count ~ site + time, data=skylark, model=2)
> index(z)
time imputed se_imp
1 1 1.0000000 0.00000000
2 2 0.8955586 0.03961601
3 3 0.9871129 0.05149670
4 4 0.9907025 0.05617083
5 5 1.0841256 0.06472818
6 6 1.1902220 0.07523418
7 7 1.2715570 0.08597312
8 8 1.3498571 0.09976989
> # mimic classic TRIM:
> index(z, "both")
time fitted se_fit imputed se_imp
1 1 1.000000 0.00000000 1.0000000 0.00000000
2 2 1.056356 0.01102452 0.8955586 0.03961601
3 3 1.115888 0.02329164 0.9871129 0.05149670
4 4 1.178776 0.03690640 0.9907025 0.05617083
5 5 1.245207 0.05198174 1.0841256 0.06472818
6 6 1.315382 0.06863904 1.1902220 0.07523418
7 7 1.389512 0.08700873 1.2715570 0.08597312
8 8 1.467820 0.10723092 1.3498571 0.09976989
> # Extract standard errors for the imputed data
> SE <- index(z,"imputed")$se_mod
> # Include covariates
> skylark$Habitat <- factor(skylark$Habitat) # hack
> z <- trim(count ~ site + time + Habitat, data=skylark, model=2)
> ind <- index(z, covars=TRUE)
> plot(ind)
Error in if (!covar %in% levels(z$covariate)) stop(sprintf("Covariate \"%s\" not present in index data", :
argument is of length zero
Calls: plot -> plot.trim.index
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-osx-x86_64, r-patched-solaris-x86
Version: 2.0.6
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘Skylark_example.Rmd’ using rmarkdown
Quitting from lines 171-172 (Skylark_example.Rmd)
Error: processing vignette 'Skylark_example.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘Skylark_example.Rmd’
--- re-building ‘rtrim_2_extensions.Rmd’ using rmarkdown
Quitting from lines 261-264 (rtrim_2_extensions.Rmd)
Error: processing vignette 'rtrim_2_extensions.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘rtrim_2_extensions.Rmd’
--- re-building ‘rtrim_confidence_intervals.Rmd’ using rmarkdown
--- finished re-building ‘rtrim_confidence_intervals.Rmd’
--- re-building ‘rtrim_for_TRIM_users.Rmd’ using rmarkdown
--- finished re-building ‘rtrim_for_TRIM_users.Rmd’
--- re-building ‘taming_overdispersion.Rmd’ using rmarkdown
--- finished re-building ‘taming_overdispersion.Rmd’
--- re-building ‘TRIM_methods_v2.pdf.asis’ using asis
--- finished re-building ‘TRIM_methods_v2.pdf.asis’
SUMMARY: processing the following files failed:
‘Skylark_example.Rmd’ ‘rtrim_2_extensions.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8
Version: 2.0.6
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘Skylark_example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 171-172 (Skylark_example.Rmd)
Error: processing vignette 'Skylark_example.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘Skylark_example.Rmd’
--- re-building ‘rtrim_2_extensions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 261-264 (rtrim_2_extensions.Rmd)
Error: processing vignette 'rtrim_2_extensions.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘rtrim_2_extensions.Rmd’
--- re-building ‘rtrim_confidence_intervals.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘rtrim_confidence_intervals.Rmd’
--- re-building ‘rtrim_for_TRIM_users.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘rtrim_for_TRIM_users.Rmd’
--- re-building ‘taming_overdispersion.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘taming_overdispersion.Rmd’
--- re-building ‘TRIM_methods_v2.pdf.asis’ using asis
--- finished re-building ‘TRIM_methods_v2.pdf.asis’
SUMMARY: processing the following files failed:
‘Skylark_example.Rmd’ ‘rtrim_2_extensions.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-osx-x86_64
Version: 2.0.6
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘Skylark_example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 171-172 (Skylark_example.Rmd)
Error: processing vignette 'Skylark_example.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘Skylark_example.Rmd’
--- re-building ‘rtrim_2_extensions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 261-264 (rtrim_2_extensions.Rmd)
Error: processing vignette 'rtrim_2_extensions.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘rtrim_2_extensions.Rmd’
--- re-building ‘rtrim_confidence_intervals.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘rtrim_confidence_intervals.Rmd’
--- re-building ‘rtrim_for_TRIM_users.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘rtrim_for_TRIM_users.Rmd’
--- re-building ‘taming_overdispersion.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘taming_overdispersion.Rmd’
--- re-building ‘TRIM_methods_v2.pdf.asis’ using asis
--- finished re-building ‘TRIM_methods_v2.pdf.asis’
SUMMARY: processing the following files failed:
‘Skylark_example.Rmd’ ‘rtrim_2_extensions.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-solaris-x86