Crash with METASPACE datasets

When processing METASPACE datasets in peaklist mode, rMSI2 crashes.

Datasets: https://metaspace2020.eu/dataset/2023-03-25_05h07m36s https://metaspace2020.eu/dataset/2023-05-12_15h13m22s https://metaspace2020.eu/dataset/2023-06-02_23h41m00s

Execution script:

proc <- rMSI2::ProcessingParameters()
data <- rMSI2::ImzMLDataDescription()
proc$preprocessing$massCalibration <- F
data$appendImzMLDataPath("/path/to/input.imzML")
data$setOutputPath("/path/to/output")
data$data_is_peaklist <- T
rMSI2::ProcessImages(proc, data)

Output:

R version 4.2.2 Patched (2022-11-10 r83330) -- "Innocent and Trusting"
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> proc <- rMSI2::ProcessingParameters()
> data <- rMSI2::ImzMLDataDescription()
> proc$preprocessing$massCalibration <- F
> data$appendImzMLDataPath("/path/to/input.imzML")
> data$setOutputPath("/path/to/output")
> data$data_is_peaklist <- T
> rMSI2::ProcessImages(proc, data)
Parsing ROI info of imzML 1 of 1
Loading image 1 of 1
Parsing XML data in imzML file...
Checking ibd UUID...OK
WARNING: Checksum validation is disabled, data may be corrupt!
Binning peaks...
33%|=================================                                           66%|==================================================================                                  | 2/3
 *** caught segfault ***
address (nil), cause 'memory not mapped'

Traceback:
 1: CRunPeakBinning(img_lst_proc, numOfThreads, memoryPerThreadMB,     proc_params$preprocessing)
 2: RunPreProcessing(proc_params, data_description$outputpath, img_lst,     data_description$data_is_peaklist, numOfThreads, memoryPerThreadMB)
 3: rMSI2::ProcessImages(proc, data)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
100%|====================================================================================================| 3/3

 *** caught segfault ***
address (nil), cause 'memory not mapped'

Traceback:
 1: CRunPeakBinning(img_lst_proc, numOfThreads, memoryPerThreadMB,     proc_params$preprocessing)
 2: RunPreProcessing(proc_params, data_description$outputpath, img_lst,     data_description$data_is_peaklist, numOfThreads, memoryPerThreadMB)
 3: rMSI2::ProcessImages(proc, data)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:

With the dataset "20230531_dv_lungatlas_nglyc_25um.imzML" this warning appears and it also fails, I'm not sure if it fails for the same reason or if it's an issue with the dataset: Warning in imzML parsing: No pixel size found!!!!!!!, assuming 1 um

prafols / rMSI2

Crash with METASPACE datasets #3