Run AMAPVox

Run AMAPVox either in batch mode or with Graphical User Interface (GUI). The function embeds a version manager for installing locally any version available remotely.

AMAPVox versions equal or prior to 1.10 require Java 8 on your Operating System. Refer to section Java 8 64-Bit for details.

gui function has been kept for background compatibility. It is an alias of the run function.

run(
  version = "latest",
  xml,
  java = "java",
  jvm.options = "-Xms2048m",
  nt = 1,
  ntt = 1,
  stdout = ""
)

gui(version = "latest", java = "java", jvm.options = "-Xms2048m", stdout = "")

Arguments

version,

either "latest" or a valid version number major.minor(.build) if version="latest" the function looks for latest remote version. If there is no internet connection it runs latest local version.

xml

path(s) to AMAPVox XML configuration files. If missing or NULL AMAPVox launches the GUI.

java

path to the java executable. Ignored for AMAPVox version >= 2.0 since Java is embedded within AMAPVox binary. Default 'java' value assumes that java is correctly defined on the $PATH variable.

jvm.options

JVM (Java Virtual Machine) options. By default it allocates 2Go of heap memory to AMAPVox.

nt

maximum number of threads for running tasks. nt=1 means sequential execution. nt=0 means as many threads as available.

ntt

maximum number of threads per task. ntt=0 means as many threads as available.

stdout

where output from both stdout/stderr should be sent. Same as stdout & stderr options from function system2().

Java 8 64-Bit

AMAPVox versions equal or prior to 1.10 rely on Java/JavaFX 64-Bit. It must be installed on the Operating System before running AMAPVox. In practice it requires either Java 8 64-Bit Oracle or Java 8 64-Bit Corretto. Mind that OpenJDK 8 will not work for AMAPVox GUI since JavaFX is not included in this distribution. Nonetheless for AMAPVox in batch mode, any version of Java 64-bit >= 8 should work.

You may check beforehand if java is installed on your system and which version.

system2("java", args = "-version")

If AMAPVox::run keeps throwing errors after you have installed a suitable Java 8 64-Bit, it means that Java 8 may not be properly detected by your system. In such case you may have to check and set the JAVA_HOME environment variable.

Sys.getenv("JAVA_HOME")
Sys.setenv(JAVA_HOME="path/to/java/8/bin")
system2("java", args = "-version")

As a last resort you may change the java parameter of this function and set the full path to Java 8 binary.

AMAPVox::run("1.10.4", java = "/path/to/java/8/bin/java")

Examples

if (FALSE) {
# (install and) run latest AMAPVox version with GUI
AMAPVox::run()
# (install and) run version 2.0.0 with GUI
AMAPVox::run(version="2.0.0")
# run latest AMAPVox version with XML configuration
AMAPVox::run(xml="/path/to/cfg.xml")
# run multiple configurations
AMAPVox::run(xml=c("cfg1.xml", "cfg2.xml"), nt=2)
}