.. data.table notation not recognized within BiocProject calls

[stolarczyk]

.. data.table notation is not recognized within BiocProject calls. See log below:

> conditions=data.table(
+         sample_name=c("SRR7629152", "SRR7629153", "SRR7629154",
+                       "SRR7629155", "SRR7629156", "SRR7629157"),
+         condition=factor(c(rep("untreated", 3),
+                            rep("treated", 3)))
+     )
> ProjectConfig="/project/shefflab/processed/pepatac/GSE117940/GSE117940_config.yaml"
> bp = BiocProject(ProjectConfig, funcArgs=list(
+     summary_dir="/project/shefflab/processed//pepatac/GSE117940/summary",
+     results_subdir="/project/shefflab/processed//pepatac/GSE117940/results_subdir",
+     genome="hg38",
+     conditions=conditions,
+     lolaPath="/project/shefflab/LOLAweb/databases/LOLACore/hg38/")
+ )
Loading config file: /project/shefflab/processed/pepatac/GSE117940/GSE117940_config.yaml
The 'bioconductor' key found in the Project config
Function 'runCOCOA' read from file '/home/mjs5kd/code/pepatac/BiocProject/runCOCOA.R'

------------------------------ Your function error ------------------------------

error 1: object '..cols' not found

--------------------------------------------------------------------------------

No data was read. The error message was returned instead: object '..cols' not found

relevant section of code:

# Subset count table by condition table
    cols <- colnames(ct)[c(TRUE ,colnames(ct) %in% conditions$sample_name)]
    ct   <- ct[,..cols] <-----

This works:

# Subset count table by condition table
    cols <- colnames(ct)[c(TRUE ,colnames(ct) %in% conditions$sample_name)]
    ct   <- ct[, cols, with=FALSE] <-----