Michael Steinbaugh

@kward Sure I'll try to test this out and get back to you

I'm seeing this issue when using the [prettier-plugin-sort-json](https://github.com/Gudahtt/prettier-plugin-sort-json) in a global install as well. The plugin doesn't get detected unless I pass it in manually: ```sh prettier --plugin '/opt/koopa/app/prettier/3.0.2/lib/node_modules/prettier-plugin-sort-json/dist/index.js' --help...

Here's a slightly more informative message from data.table's fread engine: ``` > tsv .local -> do.call -> do.call -> ```

Here's a fixed version of the file that now works with cBioPortalData in Bioconductor [data_sv.txt](https://github.com/cBioPortal/datahub/files/11434911/data_sv.txt)

@rmadupuri I noticed a few other files aren't formatted correctly. @LiNk-NY and I are putting together a list and I'll update the thread here. Thanks!!

Thanks @LiNk-NY I'll file a bug there too

Following up, I agree that it's better to fix the upstream source, but it does look like readr handles this file OK. ```r library(pipette) con

OK issue has been filed with the cBioPortal datahub team here https://github.com/cBioPortal/datahub/issues/1820

I can confirm that fixing the `data_sv.txt` file fixes this issue: https://github.com/cBioPortal/datahub/issues/1820#issuecomment-1540690313 ```r ## First, replace the `data_sv.txt` file in extracted directory. object

Seeing parsing issues for: - `blca_plasmacytoid_mskcc_2016/data_sv.txt` - `brca_tcga_pan_can_atlas_2018/data_sv.txt` - `coadread_tcga_pan_can_atlas_2018/data_sv.txt` - `ov_tcga_pan_can_atlas_2018/data_sv.txt` - `sarc_tcga_pan_can_atlas_2018/data_gene_panel_matrix.txt`