fromJSON corrupts json files

[RoganGrant]

I have run into an odd issue where it appears that loading a JSON file using fromJSON() causes the file to become corrupted without ever explicitly writing. Apologies for the large reprex file, but it seems to be more common on large files such as this one. The code to reproduce is simply:

json = jsonlite::fromJSON(filepath, flatten = TRUE)
json = json$features #unclear if this is necessary to reproduce

On running this, the file size of the json is reduced by ~20MB. If you then try to load the file again as above, it rightfully returns the following error:

Error in parse_con(txt, bigint_as_char) : parse error: premature EOF

                 (right here) ------^

Link: https://drive.google.com/file/d/1aX5nq9iOY-BTxqqIQgnoKqFiMeTaLY0a/view?usp=sharing

Thank you for your help on this and for a fantastic package!

[jeroen]

That is a huge file you posted, I wonder if your machine might be running out of memory.

Are you aware there are specialized packages for reading geojson data, which might work better? For example:

library(geojsonsf)
polygons <- geojson_sf('segmentation_polygons_2d.json')

Or with the sf package:

library(sf)
library <- st_read('segmentation_polygons_2d.json')

[RoganGrant]

Agreed, it is huge (spatial transcriptomics). This script actually comes right from 10X Genomics so I was trying to keep as close to the original as possible, but I agree this should probably be changed. As for memory: it's an instance of RStudio server on an HPC with 1TB of RAM, so likely not the issue. In any case, low priority but wanted to make you aware.

Thanks for your help!