Java heap space too small for running extract.R

[culpinnis]

The extract.R script is not able to finish its work, because the java heap space is not big enough on the test machine. We should investigate this behavior.

Running Massbank Script - Extract.R
Rscript Extract.R -f ./record
Lade nötiges Paket: rrdf
Lade nötiges Paket: rJava
Lade nötiges Paket: methods
Lade nötiges Paket: rrdflibs
log4j:WARN No appenders could be found for logger (org.apache.jena.riot.RDFLanguages).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Lade nötiges Paket: RMassBank
Lade nötiges Paket: Rcpp
Lade nötiges Paket: RCurl
Lade nötiges Paket: bitops

Attache Paket: ‘RCurl’

Das folgende Objekt ist maskiert ‘package:rJava’:

    clone

  |===============                                                       |  22%[1] "./record/Eawag/EA273251.txt"
[1] "./record/Eawag/EA273252.txt"
[1] "./record/Eawag/EA273253.txt"
[1] "./record/Eawag/EA273254.txt"
[1] "./record/Eawag/EA273255.txt"
[1] "./record/Eawag/EA273256.txt"
[1] "./record/Eawag/EA273257.txt"
[1] "./record/Eawag/EA273258.txt"
[1] "./record/Eawag/EA273259.txt"
[1] "./record/Eawag/EA273260.txt"
[1] "./record/Eawag/EA273261.txt"
[1] "./record/Eawag/EA273262.txt"
[1] "./record/Eawag/EA273263.txt"
  |=======================                                               |  32%Fehler in .jcheck() :
  java.lang.OutOfMemoryError: Java heap space.jcall("com/github/egonw/rrdf/RJenaHelper", "V", "addObjectProperty", store, subject, predicate, object)<S4 object of class "jobjRef">
Ruft auf: add.triple -> .jcall -> .jcheck -> .Call
Zusätzlich: Es gab 44 Warnungen (Anzeige mit warnings())
Ausführung angehalten

[culpinnis]

I have found a fix for this bug, but for now it requires at least 5GB of RAM. I will update the extract script as soon as possible.

[culpinnis]

Okay fixed.