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Attempt to fix datatable issue in R #289

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donaldcampbelljr wants to merge 1 commit into dev from dev_fix_r_datatable

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donaldcampbelljr commented Oct 4, 2024 •

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When using datable.table 1.16.0, PEPATACr.R was giving me an error:

Error in forderv(x, by = by, sort = FALSE, retGrp = TRUE) : 
  Column 1 passed to [f]order is type 'list', not yet supported.
Calls: <Anonymous> ... lapply -> FUN -> unique -> unique.data.table -> forderv
Execution halted

I refactored the creation of the stats data table. The project-level pipeline seems to work but now it gives me a warning:

Creating summary plots...
Warning messages:
1: In as.data.table.list(yaml_file$PEPATAC$sample[[sample_name]]) :
  Item 1 has 3 rows but longest item has 4; recycled with remainder.
2: In as.data.table.list(yaml_file$PEPATAC$sample[[sample_name]]) :
  Item 1 has 3 rows but longest item has 4; recycled with remainder

For reference, I am using an installation based on documentation here:
https://pepatac.databio.org/en/dev/detailed-install/

R version 4.1.2 (2021-11-01) -- "Bird Hippie"


          attempt to fix datatable issue in R

42a9c8f

donaldcampbelljr mentioned this pull request

PEPATACr.R now gives error with upgraded R dependencies #291

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