CRAN Package Check Results for Package shipunov

Last updated on 2024-10-14 20:50:21 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.17.1 8.00 88.16 96.16 NOTE
r-devel-linux-x86_64-debian-gcc 1.17.1 5.52 56.57 62.09 NOTE
r-devel-linux-x86_64-fedora-clang 1.17.1 160.31 NOTE
r-devel-linux-x86_64-fedora-gcc 1.17.1 148.94 ERROR
r-devel-windows-x86_64 1.17.1 9.00 136.00 145.00 NOTE
r-patched-linux-x86_64 1.17.1 10.06 83.55 93.61 NOTE
r-release-linux-x86_64 1.17.1 7.98 83.73 91.71 NOTE
r-release-macos-arm64 1.17.1 45.00 NOTE
r-release-macos-x86_64 1.17.1 88.00 NOTE
r-release-windows-x86_64 1.17.1 9.00 134.00 143.00 NOTE
r-oldrel-macos-arm64 1.17.1 49.00 OK
r-oldrel-macos-x86_64 1.17.1 84.00 OK
r-oldrel-windows-x86_64 1.17.1 9.00 159.00 168.00 OK

Check Details

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