MetFragR - Java Error

[viictoriaeriksson]

Hi,
I am trying to use the metfrag in by following the example provided by creating the "settingsObject" and use it in the run.metfrag(settingsObject). However, I never get any results from it, only gives a data frame with 0 columns/rows (but does not give any Errors). This happens both when I tried the example of a settingsObject and when I have tried to use my own input in the settingsObject.
Do you know what could be the cause for this?

Further, I have tried to use the "frag.generateMatchingFragments"-function such as:
smiles <- "CC(C(=O)C1=CC(=CC=C1)Cl)NC"
molecule<-parse.smiles(smiles)[[1]]
mzs <- c(144.080571, 145.088167, 180.057363, 182.05468)
matching.fragments<-frag.generateMatchingFragments(molecule, mzs, 197.060742, mzabs = 0.01, mzppm = 10.0, posCharge = TRUE, ionMode = 1, treeDepth = 2)

And here I obtain the error " Error in .jcall(obj, "[Lorg/openscience/cdk/interfaces/IAtomContainer;", :
java.lang.NoSuchMethodError: 'net.sf.jniinchi.INCHI_RET net.sf.jniinchi.INCHI_RET.getValue(int)' "

Therefore, I think that why also run.metfrag does not give any results, could be due to java-problem.
Have you encountered this Error before, and do you know how to solve it?

Thanks in advance!

[sneumann]

Hi, I haven't encountered this specific error before. Looks like net.sf.jniinchi.* is unavailable.
This could have to do with the rCDK installation, which also needs the InChI stuff with it.
What is your sessionInfo() ?
When trying metfRagR just now, I also had installation problems in other places having to do with Java, so there is indeed something not working, possibly in relation with newer rCDK packages.
Yours, Steffen

[sneumann]

Correction, I got your example to work here.
I did have to change two places where the JAR file is loaded.
Fixed in ec1133a
Can you give it a try and report back ?
Yours,
Steffen

> library(metfRag)
Loading required package: rJava
Loading required package: rcdk
Loading required package: rcdklibs
Loading required package: rjson
> smiles <- "CC(C(=O)C1=CC(=CC=C1)Cl)NC"
molecule<-parse.smiles(smiles)[[1]]
mzs <- c(144.080571, 145.088167, 180.057363, 182.05468)
matching.fragments<-frag.generateMatchingFragments(molecule, mzs, 197.060742, mzabs = 0.01, mzppm = 10.0, posCharge = TRUE, ionMode = 1, treeDepth = 2)

11:11:56.407 INFO  de.ipbhalle.metfraglib.process.CombinedMetFragProcess - Got 1 candidate(s)
11:11:56.465 INFO  de.ipbhalle.metfraglib.process.ProcessingStatus - 100 %
11:11:57.410 INFO  de.ipbhalle.metfraglib.process.CombinedMetFragProcess - 0 candidate(s) were discarded before processing due to pre-filtering
11:11:57.411 INFO  de.ipbhalle.metfraglib.process.CombinedMetFragProcess - 0 candidate(s) discarded during processing due to errors
11:11:57.411 INFO  de.ipbhalle.metfraglib.process.CombinedMetFragProcess - 0 candidate(s) discarded after processing due to post-filtering
11:11:57.412 INFO  de.ipbhalle.metfraglib.process.CombinedMetFragProcess - Stored 1 candidate(s)
> sessionInfo()
R version 4.3.3 (2024-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 24.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0

locale:
 [1] LC_CTYPE=en_US.UTF-8          LC_NUMERIC=C                 
 [3] LC_TIME=en_US.UTF-8           LC_COLLATE=en_US.UTF-8       
 [5] LC_MONETARY=en_US.UTF-8       LC_MESSAGES=en_US.UTF-8      
 [7] LC_PAPER=en_US.UTF-8          LC_NAME=en_US.UTF-8          
 [9] LC_ADDRESS=en_US.UTF-8        LC_TELEPHONE=en_US.UTF-8     
[11] LC_MEASUREMENT=en_US.UTF-8    LC_IDENTIFICATION=en_US.UTF-8

time zone: Europe/Berlin
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] metfRag_2.5.0 rjson_0.2.23  rcdk_3.8.1    rcdklibs_2.9  rJava_1.0-11 

loaded via a namespace (and not attached):
[1] compiler_4.3.3    squash_1.0.9      tools_4.3.3       parallel_4.3.3   
[5] fingerprint_3.5.7 iterators_1.0.14  itertools_0.1-3   png_0.1-8       

[viictoriaeriksson]

Hi,
Thank you for your reply!

I still get the same error. Here are my sessionInfo.

`Loading required package: rJava

library(metfRag)
Loading required package: rcdk
Loading required package: rcdklibs
Loading required package: rjson
Loading required package: fingerprint
smiles <- "CC(C(=O)C1=CC(=CC=C1)Cl)NC"
molecule<-parse.smiles(smiles)[[1]]
mzs <- c(144.080571, 145.088167, 180.057363, 182.05468)
matching.fragments<-frag.generateMatchingFragments(molecule, mzs, 197.060742, mzabs = 0.01, mzppm = 10.0, posCharge = TRUE, ionMode = 1, treeDepth = 2)
Error in .jcall(obj, "[Lorg/openscience/cdk/interfaces/IAtomContainer;", :
java.lang.NoSuchMethodError: 'net.sf.jniinchi.INCHI_RET net.sf.jniinchi.INCHI_RET.getValue(int)'
sessionInfo()
R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26100)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.utf8
[2] LC_CTYPE=English_United Kingdom.utf8
[3] LC_MONETARY=English_United Kingdom.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.utf8

time zone: Europe/Stockholm
tzcode source: internal

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] metfRag_2.4.2 fingerprint_3.5.7 rjson_0.2.23 rcdk_3.8.1
[5] rcdklibs_2.9 rJava_1.0-11

loaded via a namespace (and not attached):
[1] compiler_4.4.1 squash_1.0.9 parallel_4.4.1 tools_4.4.1
[5] rstudioapi_0.17.1 iterators_1.0.14 itertools_0.1-3 png_0.1-8 `

[sneumann]

Hm, so we need to check how you install, and what metfrag.jar and CDK.jar are used.
We have the same rcdk_3.8.1 rcdklibs_2.9 rJava_1.0-11. Good.
You have an older metfRag_2.4.2, can you install the most recent metfRag with my fix ?
You checkout or download the ZIP for MetFragRelaunched, and should be able to install
from within https://github.com/ipb-halle/MetFragRelaunched/tree/master/MetFragR/rpackage/metfRag
Yours,
Steffen

[viictoriaeriksson]

Thank you again for your reply!

I thought I had installed the new version, but noticed that it was not the case.
Now when I tried the newer version, I do not get the Error anymore. However, instead, I get a new Error:
"Error in frag.generateMatchingFragments(molecule, mzs, 197.060742, mzabs = 0.01, :
java.lang.ClassNotFoundException"

`Loading required package: rJava

library(metfRag)
Loading required package: rcdk
Loading required package: rcdklibs
Loading required package: rjson
smiles <- "CC(C(=O)C1=CC(=CC=C1)Cl)NC"
molecule<-parse.smiles(smiles)[[1]]
mzs <- c(144.080571, 145.088167, 180.057363, 182.05468)
matching.fragments<-frag.generateMatchingFragments(molecule, mzs, 197.060742, mzabs = 0.01, mzppm = 10.0, posCharge = TRUE, ionMode = 1, treeDepth = 2)
Error in frag.generateMatchingFragments(molecule, mzs, 197.060742, mzabs = 0.01, :
java.lang.ClassNotFoundException
sessionInfo()
R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26100)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.utf8 LC_CTYPE=English_United Kingdom.utf8 LC_MONETARY=English_United Kingdom.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.utf8

time zone: Europe/Stockholm
tzcode source: internal

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] metfRag_2.5.0 rjson_0.2.23 rcdk_3.8.1 rcdklibs_2.9 rJava_1.0-11

loaded via a namespace (and not attached):
[1] compiler_4.4.1 squash_1.0.9 parallel_4.4.1 fingerprint_3.5.7 tools_4.4.1 rstudioapi_0.17.1 iterators_1.0.14 itertools_0.1-3 png_0.1-8`