Last updated on 2023-03-23 13:52:16 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.11.1 | 71.28 | 443.87 | 515.15 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 2.11.1 | 54.24 | 325.70 | 379.94 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.11.1 | 644.31 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 2.11.1 | 647.65 | ERROR | |||
| r-patched-linux-x86_64 | 2.11.1 | 66.51 | 450.79 | 517.30 | OK | |
| r-release-linux-x86_64 | 2.11.1 | 65.47 | 430.17 | 495.64 | OK | |
| r-release-macos-arm64 | 2.11.1 | 162.00 | NOTE | |||
| r-release-macos-x86_64 | 2.11.1 | 219.00 | NOTE | |||
| r-release-windows-x86_64 | 2.11.1 | 181.00 | 1716.00 | 1897.00 | NOTE | |
| r-oldrel-macos-arm64 | 2.11.1 | 140.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 2.11.1 | 140.00 | WARN | |||
| r-oldrel-windows-ix86+x86_64 | 2.11.1 | 148.00 | 591.00 | 739.00 | NOTE |
Version: 2.11.1
Check: C++ specification
Result: NOTE
Specified C++11: please drop specification unless essential
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
Version: 2.11.1
Check: examples
Result: ERROR
Running examples in ‘phangorn-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_ci
> ### Title: Draw Confidences Intervals on Phylogenies
> ### Aliases: add_ci add_boxplot
> ### Keywords: aplot
>
> ### ** Examples
>
> data("Laurasiatherian")
> dm <- dist.hamming(Laurasiatherian)
> tree <- upgma(dm)
> set.seed(123)
> trees <- bootstrap.phyDat(Laurasiatherian,
+ FUN=function(x)upgma(dist.hamming(x)), bs=100)
> tree <- plotBS(tree, trees, "phylogram")
> tree <- plotBS(tree, trees, "phylogram")
Error in tabulate(phy$edge[, 1]) : 'bin' must be numeric or a factor
Calls: plotBS ... sapply -> lapply -> FUN -> .is.rooted_ape -> tabulate
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 2.11.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘AdvancedFeatures.Rmd’ using rmarkdown
--- finished re-building ‘AdvancedFeatures.Rmd’
--- re-building ‘Ancestral.Rmd’ using rmarkdown
--- finished re-building ‘Ancestral.Rmd’
--- re-building ‘IntertwiningTreesAndNetworks.Rmd’ using rmarkdown
--- finished re-building ‘IntertwiningTreesAndNetworks.Rmd’
--- re-building ‘MLbyHand.Rmd’ using rmarkdown
Quitting from lines 105-107 (MLbyHand.Rmd)
Error: processing vignette ‘MLbyHand.Rmd’ failed with diagnostics:
argument is of length zero
--- failed re-building ‘MLbyHand.Rmd’
--- re-building ‘Morphological.Rmd’ using rmarkdown
--- finished re-building ‘Morphological.Rmd’
--- re-building ‘Networx.Rmd’ using rmarkdown
Quitting from lines 30-38 (Networx.Rmd)
Error: processing vignette ‘Networx.Rmd’ failed with diagnostics:
argument is of length zero
--- failed re-building ‘Networx.Rmd’
--- re-building ‘Trees.Rmd’ using rmarkdown
--- finished re-building ‘Trees.Rmd’
SUMMARY: processing the following files failed:
‘MLbyHand.Rmd’ ‘Networx.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 2.11.1
Check: examples
Result: ERROR
Running examples in ‘phangorn-Ex.R’ failed
The error most likely occurred in:
> ### Name: add_ci
> ### Title: Draw Confidences Intervals on Phylogenies
> ### Aliases: add_ci add_boxplot
> ### Keywords: aplot
>
> ### ** Examples
>
> data("Laurasiatherian")
> dm <- dist.hamming(Laurasiatherian)
> tree <- upgma(dm)
> set.seed(123)
> trees <- bootstrap.phyDat(Laurasiatherian,
+ FUN=function(x)upgma(dist.hamming(x)), bs=100)
> tree <- plotBS(tree, trees, "phylogram")
> tree <- plotBS(tree, trees, "phylogram")
Error in tabulate(phy$edge[, 1]) : 'bin' must be numeric or a factor
Calls: plotBS ... sapply -> lapply -> FUN -> .is.rooted_ape -> tabulate
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 2.11.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘AdvancedFeatures.Rmd’ using rmarkdown
--- finished re-building ‘AdvancedFeatures.Rmd’
--- re-building ‘Ancestral.Rmd’ using rmarkdown
--- finished re-building ‘Ancestral.Rmd’
--- re-building ‘IntertwiningTreesAndNetworks.Rmd’ using rmarkdown
--- finished re-building ‘IntertwiningTreesAndNetworks.Rmd’
--- re-building ‘MLbyHand.Rmd’ using rmarkdown
Quitting from lines 105-107 (MLbyHand.Rmd)
Error: processing vignette 'MLbyHand.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘MLbyHand.Rmd’
--- re-building ‘Morphological.Rmd’ using rmarkdown
--- finished re-building ‘Morphological.Rmd’
--- re-building ‘Networx.Rmd’ using rmarkdown
Quitting from lines 30-38 (Networx.Rmd)
Error: processing vignette 'Networx.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘Networx.Rmd’
--- re-building ‘Trees.Rmd’ using rmarkdown
--- finished re-building ‘Trees.Rmd’
SUMMARY: processing the following files failed:
‘MLbyHand.Rmd’ ‘Networx.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 2.11.1
Check: installed package size
Result: NOTE
installed size is 7.6Mb
sub-directories of 1Mb or more:
doc 1.5Mb
libs 3.6Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Version: 2.11.1
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘AdvancedFeatures.Rmd’ using rmarkdown
Quitting from lines 280-281 (AdvancedFeatures.Rmd)
Error: processing vignette 'AdvancedFeatures.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘AdvancedFeatures.Rmd’
--- re-building ‘Ancestral.Rmd’ using rmarkdown
Error: processing vignette 'Ancestral.Rmd' failed with diagnostics:
there is no package called ‘sass’
--- failed re-building ‘Ancestral.Rmd’
--- re-building ‘IntertwiningTreesAndNetworks.Rmd’ using rmarkdown
Error: processing vignette 'IntertwiningTreesAndNetworks.Rmd' failed with diagnostics:
there is no package called ‘sass’
--- failed re-building ‘IntertwiningTreesAndNetworks.Rmd’
--- re-building ‘MLbyHand.Rmd’ using rmarkdown
Error: processing vignette 'MLbyHand.Rmd' failed with diagnostics:
there is no package called ‘sass’
--- failed re-building ‘MLbyHand.Rmd’
--- re-building ‘Morphological.Rmd’ using rmarkdown
Error: processing vignette 'Morphological.Rmd' failed with diagnostics:
there is no package called ‘sass’
--- failed re-building ‘Morphological.Rmd’
--- re-building ‘Networx.Rmd’ using rmarkdown
Error: processing vignette 'Networx.Rmd' failed with diagnostics:
there is no package called ‘sass’
--- failed re-building ‘Networx.Rmd’
--- re-building ‘Trees.Rmd’ using rmarkdown
Error: processing vignette 'Trees.Rmd' failed with diagnostics:
there is no package called ‘sass’
--- failed re-building ‘Trees.Rmd’
SUMMARY: processing the following files failed:
‘AdvancedFeatures.Rmd’ ‘Ancestral.Rmd’
‘IntertwiningTreesAndNetworks.Rmd’ ‘MLbyHand.Rmd’ ‘Morphological.Rmd’
‘Networx.Rmd’ ‘Trees.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-x86_64