SiPhyNetwork
A Phylogenetic Simulator for Reticulate Evolution
v1.1.0
·
Apr 14, 2023
·
GPL-3
Description
A simulator for reticulate evolution under a birth-death-hybridization process. Here the birth-death process is extended to consider reticulate Evolution by allowing hybridization events to occur. The general purpose simulator allows the modeling of three different reticulate patterns: lineage generative hybridization, lineage neutral hybridization, and lineage degenerative hybridization. Users can also specify hybridization events to be dependent on a trait value or genetic distance. We also extend some phylogenetic tree utility and plotting functions for networks. We allow two different stopping conditions: simulated to a fixed time or number of taxa. When simulating to a fixed number of taxa, the user can simulate under the Generalized Sampling Approach that properly simulates phylogenies when assuming a uniform prior on the root age.
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Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | NOTE |
| r-devel-linux-x86_64-debian-gcc | NOTE |
| r-devel-linux-x86_64-fedora-clang | NOTE |
| r-devel-linux-x86_64-fedora-gcc | NOTE |
| r-devel-macos-arm64 | NOTE |
| r-devel-windows-x86_64 | NOTE |
| r-oldrel-macos-arm64 | NOTE |
| r-oldrel-macos-x86_64 | NOTE |
| r-oldrel-windows-x86_64 | NOTE |
| r-patched-linux-x86_64 | NOTE |
| r-release-linux-x86_64 | NOTE |
| r-release-macos-arm64 | ERROR |
| r-release-macos-x86_64 | ERROR |
| r-release-windows-x86_64 | NOTE |
Check details (16 non-OK)
NOTE
r-devel-linux-x86_64-debian-clang
Rd files
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:72: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:73: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:70: Lost braces in \itemize; meant \describe ?
NOTE
r-devel-linux-x86_64-debian-gcc
Rd files
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:72: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:73: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:70: Lost braces in \itemize; meant \describe ?
NOTE
r-devel-linux-x86_64-fedora-clang
Rd files
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:72: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:73: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:70: Lost braces in \itemize; meant \describe ?
NOTE
r-devel-linux-x86_64-fedora-gcc
Rd files
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:72: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:73: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:70: Lost braces in \itemize; meant \describe ?
NOTE
r-devel-macos-arm64
Rd files
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:72: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:73: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:70: Lost braces in \itemize; meant \describe ?
NOTE
r-devel-windows-x86_64
Rd files
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:72: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:73: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:70: Lost braces in \itemize; meant \describe ?
NOTE
r-oldrel-macos-arm64
Rd files
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:72: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:73: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:70: Lost braces in \itemize; meant \describe ?
NOTE
r-oldrel-macos-x86_64
Rd files
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:72: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:73: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:70: Lost braces in \itemize; meant \describe ?
NOTE
r-oldrel-windows-x86_64
Rd files
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:72: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:73: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:70: Lost braces in \itemize; meant \describe ?
NOTE
r-patched-linux-x86_64
Rd files
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:72: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:73: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:70: Lost braces in \itemize; meant \describe ?
NOTE
r-release-linux-x86_64
Rd files
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:72: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:73: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:70: Lost braces in \itemize; meant \describe ?
NOTE
r-release-macos-arm64
Rd files
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:72: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:73: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:70: Lost braces in \itemize; meant \describe ?
ERROR
r-release-macos-arm64
re-building of vignette outputs
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using knitr
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
68:34: unexpected symbol
67: person(family = "de Vienne", given = c("Damien" , "M")),
68: person(family = "Sz{\\"o
^
--- failed re-building ‘introduction.Rmd’
SUMMARY: processing the following file failed:
‘introduction.Rmd’
Error: Vignette re-building failed.
Execution halted
NOTE
r-release-macos-x86_64
Rd files
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:72: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:73: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:70: Lost braces in \itemize; meant \describe ?
ERROR
r-release-macos-x86_64
re-building of vignette outputs
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using knitr
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
68:34: unexpected symbol
67: person(family = "de Vienne", given = c("Damien" , "M")),
68: person(family = "Sz{\\"o
^
--- failed re-building ‘introduction.Rmd’
SUMMARY: processing the following file failed:
‘introduction.Rmd’
Error: Vignette re-building failed.
Execution halted
NOTE
r-release-windows-x86_64
Rd files
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:72: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:73: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.ssa.Rd:70: Lost braces in \itemize; meant \describe ?
Check History
ERROR 0 OK · 12 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE Mar 9, 2026
NOTE
r-devel-linux-x86_64-debian-clang
Rd files
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: L
NOTE
r-devel-linux-x86_64-debian-gcc
Rd files
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: L
NOTE
r-devel-linux-x86_64-fedora-clang
Rd files
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: L
NOTE
r-devel-linux-x86_64-fedora-gcc
Rd files
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: L
NOTE
r-devel-macos-arm64
Rd files
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: L
NOTE
r-devel-windows-x86_64
Rd files
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: L
NOTE
r-patched-linux-x86_64
Rd files
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: L
NOTE
r-release-linux-x86_64
Rd files
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: L
ERROR
r-release-macos-arm64
Rd files
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: L
ERROR
r-release-macos-x86_64
Rd files
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: L
NOTE
r-release-windows-x86_64
Rd files
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: L
NOTE
r-oldrel-macos-arm64
Rd files
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: L
NOTE
r-oldrel-macos-x86_64
Rd files
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: L
NOTE
r-oldrel-windows-x86_64
Rd files
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: L
Dependency Network
Version History
new
1.1.0
Mar 9, 2026