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ipb-halle / MetFragR

R package for MetFrag
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rJava problem #13

Closed lucanard closed 8 years ago

lucanard commented 8 years ago

Hi

I have been trying to use the metfRag package, but unfortunately when I use the function score.molecules.from.container I alwayas get this error: "Error in .jcall(obj, "[Lorg/openscience/cdk/interfaces/IAtomContainer;", : method generateMatchingFragments with signature ([DDDZII)[Lorg/openscience/cdk/interfaces/IAtomContainer; not found"

I get a very similar error with the function getFragments. I think it is an rJava problem, but I am not able to solve it. Any idea of where this problem arises from?

c-ruttkies commented 8 years ago

Hi lucanard,

in case you still want to use metfRag R package this should be fixed now. We have upgraded to version 2.0. You can also use the run.metfrag function to query online databases. The score.molecules.from.container function has a new declaration:

score.molecules.from.container<-function(molecules, mzs, ints, exact.mass, number.threads=1, mz.abs=0.01, mz.ppm=10, pos.charge=TRUE, mode=1, tree.depth=2, score.names=c("FragmenterScore"), scoreWeights=c(1.0))

In case of further problems just let me know.

Best regards, Christoph

lucanard commented 8 years ago

Thank you very much Christoph. It seems working fine now. Waiting for the release of the manual.