FAQ.md

In richelbilderbeek/wiritttes: WIRITTE simulation

FAQ

Errors

BEAST requires Java version 8

Sometimes my Java version degrades to version 7. BEAST2 will show this:

:

Solution: on the command-line do this:

sudo apt-get install oracle-java8-set-default

This will make BEAST2 issue a warning, but you can alternively choose to use openjdk:

sudo apt-get install openjdk-8-jre

Cannot find package rBEAST

Perhaps the prerequisites are missing:

if (is.element("adephylo", installed.packages()[, 1])) {
  print("package is already installed")
} else {
  install.packages("adephylo", repos = "http://cran.uk.r-project.org")
}

Then install it like this:

if (is.element("rBEAST", installed.packages()[, 1])) {
  print("package is already installed")
} else {
  devtools::install_github("richelbilderbeek/rBEAST")
}

Cannot find xml2-config

This may happen when you install the XML package:

install.packages("XML")
[...]
checking for xml2-config... no
Cannot find xml2-config

Solution (from Stack Overflow) is to install libxml2-dev on the command line.

sudo apt-get install libxml2-dev

Note: an alternative is to use

sudo apt-get install r-cran-xml

richelbilderbeek/wiritttes documentation built on May 27, 2019, 8:14 a.m.