CRAN Package Check Results for Package rtrim

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

Check Details

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