4.5.0 does not run from Linux/R about sirius HOT 5 CLOSED

Hi Markus,

Many thanks for the quick replies! For now I added a small sh script to patRoon based on your last comment. Note that it uses SiriusCLIApplication instead of SiriusGUIApplication, took me some time to realize why headless wasn't working ;-) This also seems to work for the GUI release package.

#!/bin/sh
SIRBINPATH="$1"
JAVAPATH="$SIRBINPATH/../lib/runtime/bin/java"
LIBPATH="$SIRBINPATH/../lib"

shift

"$JAVAPATH" -Xms1G -XX:MaxRAMPercentage=85 --illegal-access=permit --add-opens java.base/java.lang=ALL-UNNAMED \
    --add-opens java.base/java.net=ALL-UNNAMED -Djava.library.path="$LIBPATH/native" \
    "-javaagent:$LIBPATH/app/agents-4.4.8.jar" -cp "$LIBPATH/app/*" \
    de.unijena.bioinf.ms.frontend.SiriusCLIApplication $@

The first shell argument should be the path to the bin directory. The other arguments are directly passed to SIRIUS.

from sirius.

Version 4.5.1 now contains a shell script for Linux that should work with R.

@rickhelmus The java command has slightly changed, so you might have to adopt to the included script.

from sirius.

Hey,
this is indeed strange. Maybe some character escaping issue when running from R or within docker. I will have a look.

from sirius.

I can reproduce the issue.

from sirius.

I am not sure if I can find out why the binary is not working with R since it is produced by the jpackage tool of the JDK.
Python and other languages I have tested are working fine.

As a quick fix you can simply bypass the binary and run java directly:

The command would be:

system2('/home/rick/Rproj/deps/sirius/lib/runtime/bin/java', args = c('-Xms1G', '-XX:MaxRAMPercentage=85', '--illegal-access=permit', '--add-opens', 'java.base/java.lang=ALL-UNNAMED', '--add-opens', 'java.base/java.net=ALL-UNNAMED', '-Djava.library.path=/home/rick/Rproj/deps/sirius/lib/native', '-javaagent:/home/rick/Rproj/deps/sirius/lib/app/agents-4.4.8.jar', '-cp', '"/home/rick/Rproj/deps/sirius/lib/app/*"', 'de.unijena.bioinf.ms.frontend.SiriusGUIApplication' , '-V'))

I used -V exemplary for the parameters of SIRIUS.

We can include a bash script launcher that is going to do the same in upcoming versions.

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