Failure with current test data

[sneumann]

The instructions in https://github.com/ipb-halle/RMassBank_mFam#test-in-docker
currently results in failures. Let's debug first.

root@734b29d1632e:/data# /usr/local/bin/msp2massbank.r "XY" test.xlsx
Loading required package: rcdklibs
Loading required package: rJava
Loading required package: Rcpp

Attaching package: ‘RMassBank’

The following objects are masked from ‘package:jsonlite’:

    flatten, validate

========================================
circlize version 0.4.11
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: https://jokergoo.github.io/circlize_book/book/

If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
  in R. Bioinformatics 2014.

This message can be suppressed by:
  suppressPackageStartupMessages(library(circlize))
========================================


Folder structure is conventional
is being created: /tmp/msp2massbank/RMassBank/MetaDataCompoundInformationProcessed.csvNew names:
* `` -> ...3
* `` -> ...5
* `` -> ...6
* `` -> ...7
* `` -> ...8
* ...

Meta data sheets are valid
Chromatography meta data is supplied
MS meta data is supplied
Fetching structures and PubChem CIDs...pre...to inchi...to CID...post...ready
Writing compound-meta-data file /tmp/msp2massbank/RMassBank/MetaDataCompoundInformationProcessed.csv
is being created :/tmp/msp2massbank/RMassBank/CompoundList_FileList.csv
 1 S3:20(5,5,10)
 2 S3:20(4,4,12)
Writing compound-list-file-list file /tmp/msp2massbank/RMassBank/CompoundList_FileList.csv
is being created: /tmp/msp2massbank/RMassBank/InfoList.csv
Processing InfoList cpd information using PubChem CID or InChI...
Processing InfoList cpd 1 / 2 using SMILES
Processing InfoList cpd 2 / 2 using SMILES
Writing info-list file /tmp/msp2massbank/RMassBank/InfoList.csv

Splitting compound list
Splitted 2 compounds into 1 settings

Creating 1 compound list part folders
is being created :/tmp/msp2massbank/RMassBank/Part_1_1__1_files__2_cpdsis being created: /tmp/msp2massbank/RMassBank/Part_1_1__1_files__2_cpds
Writing compound-list-file-list part file /tmp/msp2massbank/RMassBank/Part_1_1__1_files__2_cpds/CompoundList_1_1__1_files__2_cpds.csv
Writing info-list part file /tmp/msp2massbank/RMassBank/Part_1_1__1_files__2_cpds/InfoList_1_1__1_files__2_cpds.csv
Writing settings file /tmp/msp2massbank/RMassBank/Part_1_1__1_files__2_cpds/Settings_1_1__1_files__2_cpds.ini
################################################################################################
### Processing part 1 / 1 /tmp/msp2massbank/RMassBank/Part_1_1__1_files__2_cpds
Processing spectra mFA: 2 compounds
Loaded compoundlist successfully
  |======================================================================| 100%msmsWorkflow: Step 2. First analysis pre recalibration
  |                                                                      |   0%org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 710.3778714201
  |===================================                                   |  50%org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 710.3778714201
  |======================================================================| 100%
msmsWorkflow: Step 3. Aggregate all spectra
msmsWorkflow: Step 6. Aggregate recalibrated results
msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O
  |======================================================================| 100%
msmsWorkflow: Step 8. Peak multiplicity filtering
msmsWorkflow: Step 8. Peak multiplicity filtering skipped because multiplicityFilter parameter is not set.
msmsWorkflow: Done.
mbWorkflow: Step 1. Gather info from several databases
1: smiles
2: smiles
mbWorkflow: Step 2. Export infolist (if required)
The file ./infolist.csv was generated with new compound information. Please check and edit the table, and add it to your infolist folder.
mbWorkflow: Step 3. Data reformatting
mbWorkflow: Step 4. Spectra compilation
Compiling: S3:20(5,5,10)
Compiling: S3:20(4,4,12)
mbWorkflow: Step 5. Flattening records
mbWorkflow: Step 7. Generate subdirs and export
### Warning ### No tsv generated: No record files in folder XY/recdata_invalid 
[1] "Correcting 2 files in folder XY/recdata"
Warning in correctRecords(folder = filePath_recData_valid, applyIntensityThreshold = applyIntensityThreshold) :
  ### Peak duplicates: anno not implemented yet 45 XY/recdata/XY000167.txt
Warning in correctRecords(folder = filePath_recData_valid, applyIntensityThreshold = applyIntensityThreshold) :
  ### Peak order: anno not implemented yet 45 XY/recdata/XY000167.txt
Warning in correctRecords(folder = filePath_recData_valid, applyIntensityThreshold = applyIntensityThreshold) :
  ### Num Peak: anno not implemented yet 45 XY/recdata/XY000167.txt
[1] "Corrected XY/recdata/XY000167.txt"
Warning in correctRecords(folder = filePath_recData_valid, applyIntensityThreshold = applyIntensityThreshold) :
  ### Peak duplicates: anno not implemented yet 45 XY/recdata/XY000267.txt
Warning in correctRecords(folder = filePath_recData_valid, applyIntensityThreshold = applyIntensityThreshold) :
  ### Peak order: anno not implemented yet 45 XY/recdata/XY000267.txt
Warning in correctRecords(folder = filePath_recData_valid, applyIntensityThreshold = applyIntensityThreshold) :
  ### Num Peak: anno not implemented yet 45 XY/recdata/XY000267.txt
[1] "Corrected XY/recdata/XY000267.txt"
[1] "Correcting 0 files in folder XY/recdata_invalid"
### Warning ### No msp generated: No record files in folder XY/recdata_invalid 

Aggregate msp from 1 folders (1) msp files
Aggregate MassBank records from 1 folders
Aggregate summary records from 1 folders
Part X / XX Prec. Child Peaks
Part 1 / 1 pr TRUE; ch TRUE; pk TRUE
Postprocess summary
Collect nice summary
Postprocess nice summary
Validating 3 records in folder /tmp/msp2massbank 
Validator version: 2.1.6
Validator version: 2.1.6
14:31:20.794 ERROR massbank.cli.Validator - The peaks in the peak list are not sorted.
Error in line (150.0986,55,69).

14:31:20.800 ERROR massbank.cli.Validator - RECORD_TITLE: S3:20(5,5,10); LC-ESI-QTOF; MS2; CE: -10,-35,-60V; [M+HCOOH-H]-
14:31:20.800 ERROR massbank.cli.Validator - ^
14:31:20.802 ERROR massbank.cli.Validator - Error in '/tmp/msp2massbank/converted to MassBank/XY000167.txt'.
Validator version: 2.1.6
14:31:22.163 ERROR massbank.cli.Validator - The peaks in the peak list are not sorted.
Error in line (150.0986,55,69).

14:31:22.169 ERROR massbank.cli.Validator - RECORD_TITLE: S3:20(4,4,12); LC-ESI-QTOF; MS2; CE: -10,-35,-60V; [M+HCOOH-H]-
14:31:22.169 ERROR massbank.cli.Validator - ^
14:31:22.170 ERROR massbank.cli.Validator - Error in '/tmp/msp2massbank/converted to MassBank/XY000267.txt'.
Warning messages:
1: In loadRmbSettings(file_or_list = fileSettings_parts[[partIdx]]) :
  Your settings are outdated. Missing will be replaced by default values.
2: In updateSettings(o) :
  Your settings are outdated! The following fields were taken from default values: include_sp_tags

[korseby]

The massbank validator should be disabled in the script, validation is done after it has completed separately. I have fixed that problem. Maybe was re-introduced after this commit... https://github.com/korseby/RMassBank_mFam/tree/93580571e7958175b955adf7efe13d7f0acb0c9b