Last updated on 2024-11-21 19:53:00 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| shipunov | 1 | 9 | 3 |
| udunits2 | 13 |
Current CRAN status: ERROR: 1, NOTE: 9, OK: 3
Version: 1.17.1
Check: Rd files
Result: NOTE
checkRd: (-1) MrBayes.Rd:24: Lost braces
24 | \item{contype}{A character string; the type of consensus tree calculated from the posterior distribution of trees}{either "halfcompat" (majority-rule consensus tree) or "allcombat" (strict consensus tree)}
| ^
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-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64
Version: 1.17.1
Check: examples
Result: ERROR
Running examples in ‘shipunov-Ex.R’ failed
The error most likely occurred in:
> ### Name: keys
> ### Title: Diagnostic keys
> ### Aliases: keys
> ### Keywords: datasets
>
> ### ** Examples
>
> attach(keys)
>
> head(bracket1)
V1 V2 V3
1 1 It is an animal 2
2 1 It is a plant 3
3 2 Spiny Hedgehog
4 2 Not very spiny Swift
5 2 Not at all spiny Horse
6 3 Very woody Spruce
> head(bracket2)
V1 V2
1 1 Leaves pinnatifid
2 1 Leaves entire
3 2 Plants perennial, leaves dissected to numerous lanceolate lobes
4 2 Annual plants, leaves with narrow lobes
5 3 The compact inflorescence is surrounded by leaflike bracts
6 3 The sparse inflorescence without specialised bracts
V3
1 2
2 3
3 Polemonium L.
4 Gilia L.
5 Collomia Nutt.
6 Plox L.
> head(branched)
V1 V2
1 1 Leaves cauline.
2 2 Perennials, sometimes woody
3 2 Annuals.
4 3 Spikes glandular-hairy; all bracts similar
5 3 Spikes eglandular; proximal bracts strongly differing from distal bracts
6 1 Leaves basal.
V3
1
2 Plantago sempervirens
3
4 Plantago afra
5 Plantago arenaria
6
> head(serial)
V1 V2
1 1 6
2 2 5
3 3 4
4 4 3
5 5 2
6 6 1
V3
1 Leaves opposite. Stems with long internodes. Inflorescences nearly capitate. Capsula with 2 big seeds.
2 Annuals.
3 Bracts of lower flowers with long, narrowed appendages. Bracts of upper flowers nearly spathulate, with keel, which extend to the tip. Greyish, branching plants.
4 Bracts of lower flowers with straight appendages. Bracts of upper flowers egg-shaped, with keel, which not extend to the tip. Greenish plants, usually with rare branches.
5 Perennials with lignose stems; bracts of lower flowers are very broad, covered the most part of inflorescence base.
6 Leaves alternate, in the rosette. Inflorescences long or short cylindrical. Capsula with 12 or bigger number of seeds.
V4
1 <NA>
2 <NA>
3 Plantago arenaria
4 Plantago afra
5 Plantago sempervirens
6 <NA>
>
> ## convert keys with Biokey()
> sii <- Biokey(serial, from="serial", to="indented")
> sbb <- Biokey(serial, from="serial", to="bracket")
> bbr <- Biokey(branched, from="branched", to="bracket")
>
> ## convert keys and visualize them as trees
> library(ape) # load 'ape' library to plot Newick trees
> plot(read.tree(text=Biokey(bracket1, from="bracket", to="newick")))
> plot(read.tree(text=Biokey(bracket2, from="bracket", to="newick")))
> plot(read.tree(text=Biokey(branched, from="branched", to="newick")))
> plot(read.tree(text=Biokey(serial, from="serial", to="newick")))
>
> detach(keys)
>
> ## to make a new bracket key (without backreferences)
> ## supply three columns: id, description and 'goto'+terminal
> bracket3 <- read.table(as.is=TRUE, text="
+ 1 Small Ant
+ 1 Big 2
+ 2 Blue Sky
+ 2 Green Grass
+ ")
> bracket3
V1 V2 V3
1 1 Small Ant
2 1 Big 2
3 2 Blue Sky
4 2 Green Grass
> Biokey(bracket3, from="bracket", to="newick")
[1] "(Ant,(Sky,Grass));"
> cophenetic(ape::read.tree(text=Biokey(bracket3, from="bracket", to="newick")))
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: dist.nodes(x)
2: cophenetic.phylo(ape::read.tree(text = Biokey(bracket3, from = "bracket", to = "newick")))
3: cophenetic(ape::read.tree(text = Biokey(bracket3, from = "bracket", to = "newick")))
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-gcc
Current CRAN status: OK: 13
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